https://www.phaser.cimr.cam.ac.uk/api.php?action=feedcontributions&feedformat=atom&user=WikiSysopPhaserwiki - User contributions [en]2026-04-07T14:02:04ZUser contributionsMediaWiki 1.31.8https://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2527Course2023-10-16T12:00:31Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of Cambridge Institute for Medical Research (CIMR), University of Cambridge and the Medical Research Council Laboratory of Molecular Biology, Cambridge (MRC-LMB).<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | <b>Lecture Topics</b><br />
|-<br />
| colspan="3" | <br /><b>Basic concepts and practical aspects</b><br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space]<br />
| Randy Read<br />
| 23 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_refinement/Refinement.html Introduction to fitting, refinement and validation]<br />
| Randy Read<br />
| 14 December 1999<br />
|-<br />
| colspan="3" | <br /><b>Advanced topics</b><br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff2/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January 2000<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February 2000<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February 2000<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February 2000 <br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March 2000<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April 2000<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented <br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May 2000<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May 2000<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2526Course2023-10-16T11:59:26Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | <b>Lecture Topics</b><br />
|-<br />
| colspan="3" | <br /><b>Basic concepts and practical aspects</b><br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space]<br />
| Randy Read<br />
| 23 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_refinement/Refinement.html Introduction to fitting, refinement and validation]<br />
| Randy Read<br />
| 14 December 1999<br />
|-<br />
| colspan="3" | <br /><b>Advanced topics</b><br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff2/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January 2000<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February 2000<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February 2000<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February 2000 <br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March 2000<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April 2000<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented <br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May 2000<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May 2000<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2525Course2023-10-16T11:58:08Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space]<br />
| Randy Read<br />
| 23 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December 1999<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_refinement/Refinement.html Introduction to fitting, refinement and validation]<br />
| Randy Read<br />
| 14 December 1999<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff2/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January 2000<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February 2000<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February 2000<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February 2000 <br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March 2000<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April 2000<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented <br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May 2000<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May 2000<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May 2000<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2524Course2023-10-16T11:24:36Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space]<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_refinement/Refinement.html Introduction to fitting, refinement and validation]<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff2/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2523Course2023-10-16T11:19:18Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space]<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_refinement/Refinement.html Introduction to fitting, refinement and validation]<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2522Course2023-10-16T11:12:48Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space]<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_refinement/Refinement.html Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2521Course2023-10-16T11:10:53Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space]<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2520Course2023-10-16T11:05:36Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2519Course2023-10-16T11:04:44Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2518Course2023-10-16T11:04:30Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www-structmed.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February<br />
|-]<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2517Course2023-10-16T11:03:58Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www-structmed.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_diffraction/Diffraction.html Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_collection/Datacol.html X-ray data collection: indexing, strategy, processing]<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html The phase problem: introduction to phasing methods]<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Basic_phasing/Phasing.html Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction.html Advanced diffraction: waves, interference and complex numbers]<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_diff1/Diffraction2.html Advanced diffraction:atoms, crystals and reciprocal space]<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Fourier/Fourier.html Fourier transforms: structure factors, phases and electron density]<br />
| Randy Read<br />
| 22 February<br />
|-]<br />
| [https://www-structmed.cimr.cam.ac.uk/Course/Convolution/convolution.html The convolution theorem and its applications]<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Statistics/statistics.html Structure factor statistics: Wilson statistics, SIGMAA...]<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Likelihood/likelihood.html Maximum likelihood: theory, and application to structure refinement]<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/MolRep/molrep.html Molecular replacement]<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| [https://www.phaser.cimr.cam.ac.uk/Course/Adv_phasing/Expphasing.html Experimental phasing by maximum likelihood]<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| [https://www-structmed.cimr.cam.ac.uk/Course/DenMod/index.htm Density modification: theory and practice]<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| [https://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html Fitting, refinement and validation]<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2516Course2023-10-16T10:38:46Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview.html Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www-structmed.cimr.cam.ac.uk/Course/Crystals/intro.html Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| X-ray data collection: indexing, strategy, processing<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| The phase problem: introduction to phasing methods<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| Advanced diffraction: waves, interference and complex numbers<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| Advanced diffraction: atoms, crystals and reciprocal space<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| Fourier transforms: structure factors, phases and electron density<br />
| Randy Read<br />
| 22 February<br />
|-<br />
| The convolution theorem and its applications<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| Structure factor statistics: Wilson statistics, SIGMAA...<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| Maximum likelihood: theory, and application to structure refinement<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| Molecular replacement<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| Experimental phasing by maximum likelihood<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| Density modification: theory and practice<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| Fitting, refinement and validation<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2515Course2023-10-16T10:38:23Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [[http://www.phaser.cimr.cam.ac.uk/Course/Overview.html | Overview of X-ray crystallography]]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www-structmed.cimr.cam.ac.uk/Course/Crystals/intro.html| Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| X-ray data collection: indexing, strategy, processing<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| The phase problem: introduction to phasing methods<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| Advanced diffraction: waves, interference and complex numbers<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| Advanced diffraction: atoms, crystals and reciprocal space<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| Fourier transforms: structure factors, phases and electron density<br />
| Randy Read<br />
| 22 February<br />
|-<br />
| The convolution theorem and its applications<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| Structure factor statistics: Wilson statistics, SIGMAA...<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| Maximum likelihood: theory, and application to structure refinement<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| Molecular replacement<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| Experimental phasing by maximum likelihood<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| Density modification: theory and practice<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| Fitting, refinement and validation<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2514Course2023-10-16T10:38:01Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [http://www.phaser.cimr.cam.ac.uk/Course/Overview.html | Overview of X-ray crystallography]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| [https://www-structmed.cimr.cam.ac.uk/Course/Crystals/intro.html| Crystallisation: theory and practice]<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| [Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| X-ray data collection: indexing, strategy, processing<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| The phase problem: introduction to phasing methods<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| Advanced diffraction: waves, interference and complex numbers<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| Advanced diffraction: atoms, crystals and reciprocal space<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| Fourier transforms: structure factors, phases and electron density<br />
| Randy Read<br />
| 22 February<br />
|-<br />
| The convolution theorem and its applications<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| Structure factor statistics: Wilson statistics, SIGMAA...<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| Maximum likelihood: theory, and application to structure refinement<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| Molecular replacement<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| Experimental phasing by maximum likelihood<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| Density modification: theory and practice<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| Fitting, refinement and validation<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2513Course2023-10-16T09:53:20Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| [[Overview.html | Overview of X-ray crystallography]]<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| Crystallisation: theory and practice<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| X-ray data collection: indexing, strategy, processing<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| The phase problem: introduction to phasing methods<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| Advanced diffraction: waves, interference and complex numbers<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| Advanced diffraction: atoms, crystals and reciprocal space<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| Fourier transforms: structure factors, phases and electron density<br />
| Randy Read<br />
| 22 February<br />
|-<br />
| The convolution theorem and its applications<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| Structure factor statistics: Wilson statistics, SIGMAA...<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| Maximum likelihood: theory, and application to structure refinement<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| Molecular replacement<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| Experimental phasing by maximum likelihood<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| Density modification: theory and practice<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| Fitting, refinement and validation<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2512Course2023-10-16T09:51:52Z<p>WikiSysop: </p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.<br />
<br />
{| class="wikitable" <br />
|-<br />
! colspan="3" | Lecture Topics<br />
|-<br />
| colspan="3" | <br />Basic concepts and practical aspects<br />
|-<br />
| Overview of X-ray crystallography<br />
| Randy Read<br />
| 9 November<br />
|-<br />
| Crystallisation: theory and practice<br />
| Airlie McCoy<br />
| 16 November<br />
|-<br />
| Basic diffraction theory: waves, interference, reciprocal space<br />
| Randy Read<br />
| 23 November<br />
|-<br />
| X-ray data collection: indexing, strategy, processing<br />
| Andrew Leslie<br />
| 30 November<br />
|-<br />
| The phase problem: introduction to phasing methods<br />
| Randy Read<br />
| 7 December<br />
|-<br />
| Introduction to fitting, refinement and validation<br />
| Randy Read<br />
| 14 December<br />
|-<br />
| colspan="3" | <br />Advanced topics<br />
|-<br />
| Advanced diffraction: waves, interference and complex numbers<br />
| Randy Read<br />
| 18 January<br />
|-<br />
| Advanced diffraction: atoms, crystals and reciprocal space<br />
| Randy Read<br />
| 25 January<br />
|-<br />
| X-ray sources: from generators to synchrotrons<br />
| Gwyndaf Evans<br />
| 8 February<br />
|-<br />
| Data collection, processing, complications<br />
| Andrew Leslie<br />
| 15 February<br />
|-<br />
| Fourier transforms: structure factors, phases and electron density<br />
| Randy Read<br />
| 22 February<br />
|-<br />
| The convolution theorem and its applications<br />
| Randy Read<br />
| 29 February<br />
|-<br />
| Symmetry in real and reciprocal space<br />
| Anne Bloomer<br />
| 7 March<br />
|-<br />
| The Patterson function and its implications<br />
| Phil Evans<br />
| 28 March<br />
|-<br />
| Structure factor statistics: Wilson statistics, SIGMAA...<br />
| Randy Read<br />
| 4 April<br />
|-<br />
| Maximum likelihood: theory, and application to structure refinement<br />
| Randy Read<br />
| 11 April<br />
|-<br />
| Molecular replacement<br />
| Randy Read<br />
| 18 April<br />
|-<br />
| Isomorphous replacement<br />
| Randy Read<br />
| 25 April<br />
|-<br />
| Experimental phasing by maximum likelihood<br />
| Randy Read<br />
| not presented<br />
|-<br />
| Anomalous scattering and MAD<br />
| Gwyndaf Evans<br />
| 2 May<br />
|-<br />
| Density modification: theory and practice<br />
| Randy Read<br />
| 9 May<br />
|-<br />
| Fitting, refinement and validation<br />
| Phil Evans<br />
| 16 May<br />
|-<br />
| Analysing protein structures<br />
| Arthur Lesk<br />
| 23 May<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Course&diff=2511Course2023-10-16T09:49:27Z<p>WikiSysop: Created page with "The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB."</p>
<hr />
<div>The Macromolecular Crystallography course was presented in the 1999-2000 academic year to staff and students of CIMR, University of Cambridge and the MRC-LMB.</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=MediaWiki:Sidebar&diff=2510MediaWiki:Sidebar2023-10-16T09:48:07Z<p>WikiSysop: Add the www-structmed course pages since this website is going down</p>
<hr />
<div>** Phaser Crystallographic Software | PhaserWiki Home<br />
** Releases | Releases<br />
** Downloads | Downloads<br />
** Manuals | Manuals<br />
** Tutorials | Tutorials<br />
** FAQ | FAQ<br />
** Top Ten Tips | Top Ten Tips<br />
** Publications | Publications<br />
** External Links | External Links<br />
*users<br />
** Molecular Replacement | MR Phasing<br />
** Experimental Phasing | SAD Phasing<br />
** Course | Structmed Course<br />
*developers<br />
** Python Interface | Python Interface<br />
** Contact | Contact Developers<br />
** Developers | Developer Pages<br />
** Licences | Licences<br />
** Source Code | Source Code<br />
** phasertng | phasertng<br />
** dtmin | dtmin</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1795Airlie J. McCoy2013-07-17T11:25:31Z<p>WikiSysop: /* Publications */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5159 '''Acta Cryst D''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5142 '''Acta Cryst D''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5186 '''Acta Cryst D''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5095 '''Acta Cryst''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5108 '''Acta Cryst D''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://scripts.iucr.org/cgi-bin/paper?gx5042.pdf '''Acta Cryst D'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ys0029.pdf '''J Synch Radia''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://scripts.iucr.org/cgi-bin/paper?wd5000.pdf '''Acta Cryst D''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''Acta Cryst D''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://dx.doi.org/10.1093/protein/13.8.565 '''doi'''] Digital Object Identifier<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Publications&diff=1794Publications2013-07-17T11:20:16Z<p>WikiSysop: /* Primary Citations */</p>
<hr />
<div>[[Image:PDF_download.png| link=]] PDF downloads available <br />
==Citation==<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ<br />
:J. Appl. Cryst. (2007). 40, 658-674<br />
<br />
==Reviews==<br />
;Overview of the CCP4 suite and current developments [http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
<br />
;Using SAD data in Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5159 '''Acta Cryst D''']<br />
:Read RJ, McCoy AJ<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls [http://scripts.iucr.org/cgi-bin/paper?ba5142.pdf '''Acta Cryst D''']<br />
:McCoy AJ, Read RJ<br />
:Acta Cryst. (2010) D66, 458-469.<br />
<br />
;An introduction to molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5108 '''Acta Cryst D''']<br />
:Evans P, McCoy A<br />
:Acta Cryst.(2008) D64, 1-10. Epub 2007 Dec 5.<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D''']<br />
:McCoy AJ<br />
:Acta Cryst. (2007). D63, 32-41<br />
<br />
;Liking Likelihood [http://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']<br />
:McCoy AJ<br />
:Acta Cryst. (2004). D60, 2169-2183<br />
<br />
==Primary Citations==<br />
<br />
;Intensity statistics in the presence of translational non-crystallographic symmetry [http://scripts.iucr.org/cgi-bin/paper?dz5268 '''Acta Cryst D''']<br />
:Read RJ, Adams PD, McCoy AJ<br />
:Acta Cryst. (2013). D69, 176-183<br />
<br />
;Improvement of molecular replacement models with ''Sculptor'' [http://scripts.iucr.org/cgi-bin/paper?ba5163 '''Acta Cryst D''']<br />
:Bunkoczi G, Read RJ<br />
:Acta Cryst. (2011). D67, 303-312<br />
<br />
;Likelihood-enhanced fast translation functions [http://scripts.iucr.org/cgi-bin/paper?gx5042 '''Acta Cryst D''']<br />
:McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ<br />
:Acta Cryst. (2005). D61, 458-464<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function [http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
:McCoy AJ, Storoni LC, Read RJ<br />
:Acta Cryst. (2004). D60, 1220-1228<br />
<br />
;Likelihood-enhanced fast rotation functions [http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D''']<br />
:Acta Cryst. (2004). D60, 432-438<br />
: Storoni LC, McCoy AJ, Read RJ<br />
<br />
;Pushing the boundaries of molecular replacement with maximum likelihood [http://scripts.iucr.org/cgi-bin/paper?ba5014r '''Acta Cryst D''']<br />
:Read RJ<br />
:Acta Cryst. (2001). D57, 1373-1382</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Publications&diff=1793Publications2013-07-17T11:18:45Z<p>WikiSysop: /* Reviews */</p>
<hr />
<div>[[Image:PDF_download.png| link=]] PDF downloads available <br />
==Citation==<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ<br />
:J. Appl. Cryst. (2007). 40, 658-674<br />
<br />
==Reviews==<br />
;Overview of the CCP4 suite and current developments [http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
<br />
;Using SAD data in Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5159 '''Acta Cryst D''']<br />
:Read RJ, McCoy AJ<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls [http://scripts.iucr.org/cgi-bin/paper?ba5142.pdf '''Acta Cryst D''']<br />
:McCoy AJ, Read RJ<br />
:Acta Cryst. (2010) D66, 458-469.<br />
<br />
;An introduction to molecular replacement [http://scripts.iucr.org/cgi-bin/paper?ba5108 '''Acta Cryst D''']<br />
:Evans P, McCoy A<br />
:Acta Cryst.(2008) D64, 1-10. Epub 2007 Dec 5.<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser [http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D''']<br />
:McCoy AJ<br />
:Acta Cryst. (2007). D63, 32-41<br />
<br />
;Liking Likelihood [http://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']<br />
:McCoy AJ<br />
:Acta Cryst. (2004). D60, 2169-2183<br />
<br />
==Primary Citations==<br />
<br />
;Intensity statistics in the presence of translational non-crystallographic symmetry [http://www.phaser.cimr.cam.ac.uk/images/c/cf/Dz5268.pdf pdf]<br />
:Read RJ, Adams PD, McCoy AJ<br />
:Acta Cryst. (2013). D69, 176-183<br />
<br />
;Improvement of molecular replacement models with ''Sculptor'' [http://www.phaser.cimr.cam.ac.uk/images/3/35/Ba5163.pdf pdf]<br />
:Bunkoczi G, Read RJ<br />
:Acta Cryst. (2011). D67, 303-312<br />
<br />
;Likelihood-enhanced fast translation functions [http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ<br />
:Acta Cryst. (2005). D61, 458-464<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function [http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
:McCoy AJ, Storoni LC, Read RJ<br />
:Acta Cryst. (2004). D60, 1220-1228<br />
<br />
;Likelihood-enhanced fast rotation functions [http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D''']<br />
:Acta Cryst. (2004). D60, 432-438<br />
: Storoni LC, McCoy AJ, Read RJ<br />
<br />
;Pushing the boundaries of molecular replacement with maximum likelihood [http://www.phaser.cimr.cam.ac.uk/images/a/a6/Ba5014r.pdf pdf]<br />
:Read RJ<br />
:Acta Cryst. (2001). D57, 1373-1382</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1792Airlie J. McCoy2013-07-17T11:15:52Z<p>WikiSysop: /* 2010 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5142 '''Acta Cryst D''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5186 '''Acta Cryst D''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5095 '''Acta Cryst''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://dx.doi.org/10.1093/protein/13.8.565 '''doi'''] Digital Object Identifier<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1791Airlie J. McCoy2013-07-17T11:13:16Z<p>WikiSysop: /* 2000 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5095 '''Acta Cryst''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://dx.doi.org/10.1093/protein/13.8.565 '''doi'''] Digital Object Identifier<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Publications&diff=1790Publications2013-07-17T11:07:48Z<p>WikiSysop: /* Primary Citations */</p>
<hr />
<div>[[Image:PDF_download.png| link=]] PDF downloads available <br />
==Citation==<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ<br />
:J. Appl. Cryst. (2007). 40, 658-674<br />
<br />
==Reviews==<br />
;Overview of the CCP4 suite and current developments [http://scripts.iucr.org/cgi-bin/paper?dz5219 '''pdf''']<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
<br />
;Using SAD data in Phaser [http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''pdf''']<br />
:Read RJ, McCoy AJ<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls [http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf pdf]<br />
:McCoy AJ, Read RJ<br />
:Acta Cryst. (2010) D66, 458-469.<br />
<br />
;An introduction to molecular replacement [http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf pdf]<br />
:Evans P, McCoy A<br />
:Acta Cryst.(2008) D64, 1-10. Epub 2007 Dec 5.<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser [http://www.phaser.cimr.cam.ac.uk/images/4/40/Ba5095.pdf pdf]<br />
:McCoy AJ<br />
:Acta Cryst. (2007). D63, 32-41<br />
<br />
;Liking Likelihood [http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf pdf ]<br />
:McCoy AJ<br />
:Acta Cryst. (2004). D60, 2169-2183<br />
<br />
==Primary Citations==<br />
<br />
;Intensity statistics in the presence of translational non-crystallographic symmetry [http://www.phaser.cimr.cam.ac.uk/images/c/cf/Dz5268.pdf pdf]<br />
:Read RJ, Adams PD, McCoy AJ<br />
:Acta Cryst. (2013). D69, 176-183<br />
<br />
;Improvement of molecular replacement models with ''Sculptor'' [http://www.phaser.cimr.cam.ac.uk/images/3/35/Ba5163.pdf pdf]<br />
:Bunkoczi G, Read RJ<br />
:Acta Cryst. (2011). D67, 303-312<br />
<br />
;Likelihood-enhanced fast translation functions [http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ<br />
:Acta Cryst. (2005). D61, 458-464<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function [http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
:McCoy AJ, Storoni LC, Read RJ<br />
:Acta Cryst. (2004). D60, 1220-1228<br />
<br />
;Likelihood-enhanced fast rotation functions [http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D''']<br />
:Acta Cryst. (2004). D60, 432-438<br />
: Storoni LC, McCoy AJ, Read RJ<br />
<br />
;Pushing the boundaries of molecular replacement with maximum likelihood [http://www.phaser.cimr.cam.ac.uk/images/a/a6/Ba5014r.pdf pdf]<br />
:Read RJ<br />
:Acta Cryst. (2001). D57, 1373-1382</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1789Airlie J. McCoy2013-07-17T11:06:28Z<p>WikiSysop: /* 2004 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5095 '''Acta Cryst''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/1/19/Dolezal_etal_2000.pdf '''download pdf''']<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1788Airlie J. McCoy2013-07-17T11:04:14Z<p>WikiSysop: /* 2009 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5095 '''Acta Cryst''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf '''download pdf''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf '''download pdf''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/1/19/Dolezal_etal_2000.pdf '''download pdf''']<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1787Airlie J. McCoy2013-07-17T11:02:38Z<p>WikiSysop: /* 2004 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf '''download pdf''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf '''download pdf''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/1/19/Dolezal_etal_2000.pdf '''download pdf''']<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1786Airlie J. McCoy2013-07-17T11:02:13Z<p>WikiSysop: /* 2011 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''Acta Cryst D''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf '''download pdf''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''download pdf''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf '''download pdf''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/1/19/Dolezal_etal_2000.pdf '''download pdf''']<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1785Airlie J. McCoy2013-07-17T11:01:52Z<p>WikiSysop: /* 2007 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''download pdf''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5095 '''Acta Cryst D'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf '''download pdf''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''download pdf''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf '''download pdf''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/1/19/Dolezal_etal_2000.pdf '''download pdf''']<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1784Airlie J. McCoy2013-07-17T10:59:33Z<p>WikiSysop: /* 2002 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''download pdf''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/40/Ba5095.pdf '''download pdf'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf '''download pdf''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''download pdf''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf '''download pdf''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ba5027 '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/1/19/Dolezal_etal_2000.pdf '''download pdf''']<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1783Airlie J. McCoy2013-07-17T10:55:33Z<p>WikiSysop: /* 2011 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://scripts.iucr.org/cgi-bin/paper?dz5219 '''download pdf''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/40/Ba5095.pdf '''download pdf'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf '''download pdf''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''download pdf''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf '''download pdf''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/dc/Ba5027.pdf '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/1/19/Dolezal_etal_2000.pdf '''download pdf''']<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Publications&diff=1782Publications2013-07-17T10:55:02Z<p>WikiSysop: /* Reviews */</p>
<hr />
<div>[[Image:PDF_download.png| link=]] PDF downloads available <br />
==Citation==<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ<br />
:J. Appl. Cryst. (2007). 40, 658-674<br />
<br />
==Reviews==<br />
;Overview of the CCP4 suite and current developments [http://scripts.iucr.org/cgi-bin/paper?dz5219 '''pdf''']<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
<br />
;Using SAD data in Phaser [http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''pdf''']<br />
:Read RJ, McCoy AJ<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls [http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf pdf]<br />
:McCoy AJ, Read RJ<br />
:Acta Cryst. (2010) D66, 458-469.<br />
<br />
;An introduction to molecular replacement [http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf pdf]<br />
:Evans P, McCoy A<br />
:Acta Cryst.(2008) D64, 1-10. Epub 2007 Dec 5.<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser [http://www.phaser.cimr.cam.ac.uk/images/4/40/Ba5095.pdf pdf]<br />
:McCoy AJ<br />
:Acta Cryst. (2007). D63, 32-41<br />
<br />
;Liking Likelihood [http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf pdf ]<br />
:McCoy AJ<br />
:Acta Cryst. (2004). D60, 2169-2183<br />
<br />
==Primary Citations==<br />
<br />
;Intensity statistics in the presence of translational non-crystallographic symmetry [http://www.phaser.cimr.cam.ac.uk/images/c/cf/Dz5268.pdf pdf]<br />
:Read RJ, Adams PD, McCoy AJ<br />
:Acta Cryst. (2013). D69, 176-183<br />
<br />
;Improvement of molecular replacement models with ''Sculptor'' [http://www.phaser.cimr.cam.ac.uk/images/3/35/Ba5163.pdf pdf]<br />
:Bunkoczi G, Read RJ<br />
:Acta Cryst. (2011). D67, 303-312<br />
<br />
;Likelihood-enhanced fast translation functions [http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ<br />
:Acta Cryst. (2005). D61, 458-464<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function [http://scripts.iucr.org/cgi-bin/paper?ea5015 pdf]<br />
:McCoy AJ, Storoni LC, Read RJ<br />
:Acta Cryst. (2004). D60, 1220-1228<br />
<br />
;Likelihood-enhanced fast rotation functions [http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf pdf]<br />
:Acta Cryst. (2004). D60, 432-438<br />
: Storoni LC, McCoy AJ, Read RJ<br />
<br />
;Pushing the boundaries of molecular replacement with maximum likelihood [http://www.phaser.cimr.cam.ac.uk/images/a/a6/Ba5014r.pdf pdf]<br />
:Read RJ<br />
:Acta Cryst. (2001). D57, 1373-1382</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Airlie_J._McCoy&diff=1781Airlie J. McCoy2013-07-17T10:53:32Z<p>WikiSysop: /* 2004 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==Publications==<br />
===2013===<br />
;Intensity statistics in the presence of translational noncrystallographic symmetry.<br />
:Read RJ, Adams PD, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:Acta Crystallogr D Biol Crystallogr 2013 Feb;69(Pt 2):176-83. Epub Jan 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565438/pdf/d-69-00176.pdf '''download pdf''']<br />
<br />
===2012===<br />
;Graphical tools for macromolecular crystallography in PHENIX.<br />
:Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.<br />
:J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359726/pdf/j-45-00581.pdf '''download pdf''']<br />
<br />
===2011===<br />
;The Phenix software for automated determination of macromolecular structures.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.<br />
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3193589/pdf/nihms319608.pdf '''download pdf''']<br />
<br />
;Overview of the CCP4 suite and current developments<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, <span style="color:darkmagenta">McCoy A</span>, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e4/Dz5219.pdf '''download pdf''']<br />
<br />
;Using SAD data in Phaser<br />
:Read RJ, <span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''download pdf''']<br />
<br />
===2010===<br />
;A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.<br />
:Jackson LP, Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.<br />
:Cell. 2010 Jun 25;141(7):1220-9.<br />
:[http://www.cell.com/abstract/S0092-8674(10)00542-8 '''Cell'''] (subscription required)<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls.<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. Epub 2010 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf '''download pdf''']<br />
<br />
;PHENIX<nowiki>:</nowiki> a comprehensive Python-based system for macromolecular structure solution.<br />
:Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.<br />
:Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010 Jan 22.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b9/Dz5186.pdf '''download pdf''']<br />
<br />
===2009===<br />
;Decision-making in structure solution using Bayesian estimates of map quality<nowiki>:</nowiki> the PHENIX AutoSol wizard <br />
:Terwilliger TC, Adams PD, Read RJ, <span style="color:darkmagenta">McCoy AJ</span> , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.<br />
:Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
===2008===<br />
;A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex<br />
:Kelly BT, <span style="color:darkmagenta">McCoy AJ</span>, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.<br />
:Nature. 2008 Dec 18;456(7224):976-79<br />
:[http://www.nature.com/nature/journal/v456/n7224/abs/nature07422.html '''Nature'''] (subscription required)<br />
<br />
;An introduction to molecular replacement <br />
:Evans P, <span style="color:darkmagenta">McCoy A</span>.<br />
:Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf '''download pdf''']<br />
<br />
;Automated structure solution with the PHENIX suite<br />
:Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD.<br />
:Methods Mol Biol. 2008;426:419-35.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/8/8d/Zwart_etal_2008_preview.pdf '''preview pdf'''] [http://dx.doi.org/10.1007/978-1-60327-058-8 '''doi'''] Digital Object Identifier<br />
<br />
===2007===<br />
;A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles <br />
:Miller SE, Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Robinson MS, Owen DJ.<br />
:Nature. 2007 Nov 22;450(7169):570-4<br />
:[http://www.nature.com/nature/journal/v450/n7169/abs/nature06353.html '''Nature'''] (subscription required)<br />
<br />
;High-resolution structure prediction and the crystallographic phase problem <br />
:Qian B, Raman S, Das R, Bradley P, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ, Baker D.<br />
:Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.<br />
:[http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html '''Nature'''] (subscription required)<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/40/Ba5095.pdf '''download pdf'''] <br />
<br />
;Phaser crystallographic software <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf '''download pdf''']<br />
<br />
;β-Edge interactions in a pentadecameric human antibody Vκ domain.<br />
:James LC, Jones PC, <span style="color:darkmagenta">McCoy A</span>, Tennent GA, Pepys MB, Famm K, Winter G.<br />
:J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.<br />
:[http://dx.doi.org/10.1016/j.jmb.2006.10.093 '''doi'''] Digital Object Identifier<br />
<br />
===2006===<br />
<br />
;Crystal structure of rab11 in complex with rab11 family interacting protein 2 <br />
:Jagoe WN, Lindsay AJ, Read RJ, <span style="color:darkmagenta">McCoy AJ</span>, McCaffrey MW, Khan AR.<br />
:Structure. 2006 Aug;14(8):1273-83.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0969212606002930 '''Structure'''] (subscription required)<br />
<br />
===2005===<br />
;Likelihood-enhanced fast translation functions <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Grosse-Kunstleve RW, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf '''download pdf'''] <br />
<br />
===2004===<br />
;Liking Likelihood <br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf '''download pdf''']<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Storoni LC, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.<br />
:[http://scripts.iucr.org/cgi-bin/paper?ea5015 '''download pdf''']<br />
<br />
;Likelihood-enhanced fast rotation functions <br />
:Storoni LC, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf '''download pdf''']<br />
<br />
===2003===<br />
;Recent developments in the PHENIX software for automated crystallographic structure determination<br />
:Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.<br />
:J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e/Ys0029.pdf '''download pdf''']<br />
<br />
;Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing<br />
:Pannu NS, <span style="color:darkmagenta">McCoy AJ</span>, Read RJ.<br />
:Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/6/61/Wd5000.pdf '''download pdf''']<br />
<br />
;Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Pei XY, Skinner R, Abrahams JP, Carrell RW.<br />
:J Mol Biol. 2003 Feb 21;326(3):823-33.<br />
:[http://dx.doi.org/10.1016/S0022-2836(02)01382-7 '''doi'''] Digital Object Identifier<br />
<br />
===2002===<br />
;New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.<br />
:[http://dx.doi.org/10.1016/S0959-440X(02)00373-1 '''doi'''] Digital Object Identifier<br />
<br />
;PHENIX<nowiki>:</nowiki> building new software for automated crystallographic structure determination <br />
:Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, <span style="color:darkmagenta">McCoy AJ</span>, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.<br />
:Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/d/dc/Ba5027.pdf '''download pdf''']<br />
<br />
;Molecular architecture and functional model of the endocytic AP2 complex <br />
:Collins BM, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Evans PR, Owen DJ.<br />
:Cell. 2002 May 17;109(4):523-35.<br />
:[http://www.structure.org/content/article/abstract?uid=PIIS0092867402007353 '''Cell'''] (subscription required)<br />
<br />
===2001===<br />
:No publications<br />
<br />
===2000===<br />
;ScFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers <br />
:Dolezal O, Pearce LA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Hudson PJ, Kortt AA.<br />
:Protein Eng. 2000 Aug;13(8):565-74.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/1/19/Dolezal_etal_2000.pdf '''download pdf''']<br />
<br />
;The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions. <br />
:Huntington JA*, <span style="color:darkmagenta">McCoy A</span>*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Biol Chem. 2000 May 19;275(20):15377-83<br />
:[http://www.phaser.cimr.cam.ac.uk/images/4/45/JBC-2000-Huntington-15377-83.pdf '''download pdf''']<br />
<br />
===1999===<br />
;Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod <br />
:<span style="color:darkmagenta">McCoy AJ</span>, Fucini P, Noegel AA, Stewart M.<br />
:Nat Struct Biol. 1999 Sep;6(9):836-41.<br />
:[http://www.nature.com/nsmb/journal/v6/n9/abs/nsb0999_836.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
;scFv multimers of the anti-neuraminidase antibody NC10<nowiki>:</nowiki> length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies<br />
:Atwell JL, Breheney KA, Lawrence LJ, <span style="color:darkmagenta">McCoy AJ</span>, Kortt AA, Hudson PJ.<br />
:Protein Eng. 1999 Jul;12(7):597-604.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/e/e3/Atwell_etal_1999.pdf '''download pdf''']<br />
<br />
;Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import<br />
:Kent HM, Moore MS, Quimby BB, Baker AM, <span style="color:darkmagenta">McCoy AJ</span>, Murphy GA, Corbett AH, Stewart M.<br />
:J Mol Biol. 1999 Jun 11;289(3):565-77.<br />
:[http://dx.doi.org/10.1006/jmbi.1999.2775 '''doi'''] Digital Object Identifier<br />
<br />
===1998===<br />
;The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Dec 18;284(5):1517-27.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.2204 '''doi'''] Digital Object Identifier<br />
<br />
;Three-dimensional structures of single-chain Fv-neuraminidase complexes<br />
:Malby RL*, <span style="color:darkmagenta">McCoy AJ</span>*, Kortt AA, Hudson PJ, Colman PM.<br />
:<nowiki>*</nowiki>authors contributed equally<br />
:J Mol Biol. 1998 Jun 19;279(4):901-10.<br />
:[http://dx.doi.org/10.1006/jmbi.1998.1794 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran<br />
:Stewart M, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>.<br />
:J Mol Biol. 1998 Apr 3;277(3):635-46.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1602 '''doi'''] Digital Object Identifier<br />
<br />
;Structural basis for amoeboid motility in nematode sperm <br />
:Bullock TL, <span style="color:darkmagenta">McCoy AJ</span>, Kent HM, Roberts TM, Stewart M.<br />
:Nat Struct Biol. 1998 Mar;5(3):184-9.<br />
:[http://www.nature.com/nsmb/journal/v5/n3/abs/nsb0398-184.html '''Nature Structural Biology'''] (subscription required)<br />
<br />
===1997===<br />
;Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)<br />
:Fucini P, <span style="color:darkmagenta">McCoy AJ</span>, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.<br />
:J Struct Biol. 1997 Nov;120(2):192-5<br />
:[http://dx.doi.org/10.1006/jsbi.1997.3930 '''doi'''] Digital Object Identifier<br />
<br />
;Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran<br />
:Clarkson WD, Corbett AH, Paschal BM, Kent HM, <span style="color:darkmagenta">McCoy AJ</span>, Gerace L, Silver PA, Stewart M.<br />
:J Mol Biol. 1997 Oct 10;272(5):716-30.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1255 '''doi'''] Digital Object Identifier<br />
<br />
;The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from ''Psophocarpus tetragonolobus (L.) DC''<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Kortt AA.<br />
:J Mol Biol. 1997 Jun 27;269(5):881-91.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.1067 '''doi'''] Digital Object Identifier<br />
<br />
;Electrostatic complementarity at protein/protein interfaces<br />
:<span style="color:darkmagenta">McCoy AJ</span>, Chandana Epa V, Colman PM.<br />
:J Mol Biol. 1997 May 2;268(2):570-84.<br />
:[http://dx.doi.org/10.1006/jmbi.1997.0987 '''doi'''] Digital Object Identifier<br />
<br />
;Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer <br />
:Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, <span style="color:darkmagenta">McCoy AJ</span>, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.<br />
:Protein Eng. 1997 Apr;10(4):423-33.<br />
:[http://www.phaser.cimr.cam.ac.uk/images/f/f8/Kortt_etal_1997.pdf '''download pdf''']<br />
<br />
===1996===<br />
;Protein Structure and Interaction<br />
:<span style="color:darkmagenta">McCoy AJ</span><br />
:Thesis (Ph. D) <br />
:[http://cat.lib.unimelb.edu.au/search~S30?/amccoy+aj/amccoy+aj/-3%2C0%2C0%2CB/frameset&FF=amccoy+airlie+janet&1%2C1%2C/indexsort=- '''University of Melbourne Library'''] (not available for loan)<br />
<br />
===Other Real McCoys===<br />
{|border="1" cellpadding="10" align="left" style="color:black; background-color:#ffffee;" <br />
|<br />
There are '''four''' other AJ McCoys publishing in biomedical science and cited in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]<br />
#Andrea J. McCoy − ''University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA'' and latterly also ''Division of Bacterial Pathogenesis, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan''<br />
#Almedia J. McCoy − ''East Carolina University, Greenville, NC USA''<br />
#Austin J. McCoy − ''Vanderbilt University, Nashville, TN USA''<br />
#A. Jeanene McCoy − ''Disney's Animal Programs, Walt Disney World Resort, FL USA''<br />
Thus an author search for '''McCoy AJ''' in [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] will lead to a combined publication list for all '''five''' of us. Only the publications listed above are '''this''' real McCoy's!<br />
|}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Publications&diff=1780Publications2013-07-17T10:44:18Z<p>WikiSysop: /* Primary Citations */</p>
<hr />
<div>[[Image:PDF_download.png| link=]] PDF downloads available <br />
==Citation==<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ<br />
:J. Appl. Cryst. (2007). 40, 658-674<br />
<br />
==Reviews==<br />
;Overview of the CCP4 suite and current developments [http://www.phaser.cimr.cam.ac.uk/images/e/e4/Dz5219.pdf '''pdf''']<br />
:Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS.<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-242<br />
<br />
;Using SAD data in Phaser [http://www.phaser.cimr.cam.ac.uk/images/8/89/Ba5159.pdf '''pdf''']<br />
:Read RJ, McCoy AJ<br />
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344<br />
<br />
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls [http://www.phaser.cimr.cam.ac.uk/images/d/d3/Ba5142.pdf pdf]<br />
:McCoy AJ, Read RJ<br />
:Acta Cryst. (2010) D66, 458-469.<br />
<br />
;An introduction to molecular replacement [http://www.phaser.cimr.cam.ac.uk/images/8/86/Ba5108.pdf pdf]<br />
:Evans P, McCoy A<br />
:Acta Cryst.(2008) D64, 1-10. Epub 2007 Dec 5.<br />
<br />
;Solving structures of protein complexes by molecular replacement with Phaser [http://www.phaser.cimr.cam.ac.uk/images/4/40/Ba5095.pdf pdf]<br />
:McCoy AJ<br />
:Acta Cryst. (2007). D63, 32-41<br />
<br />
;Liking Likelihood [http://www.phaser.cimr.cam.ac.uk/images/4/46/Ba5064.pdf pdf ]<br />
:McCoy AJ<br />
:Acta Cryst. (2004). D60, 2169-2183<br />
<br />
==Primary Citations==<br />
<br />
;Intensity statistics in the presence of translational non-crystallographic symmetry [http://www.phaser.cimr.cam.ac.uk/images/c/cf/Dz5268.pdf pdf]<br />
:Read RJ, Adams PD, McCoy AJ<br />
:Acta Cryst. (2013). D69, 176-183<br />
<br />
;Improvement of molecular replacement models with ''Sculptor'' [http://www.phaser.cimr.cam.ac.uk/images/3/35/Ba5163.pdf pdf]<br />
:Bunkoczi G, Read RJ<br />
:Acta Cryst. (2011). D67, 303-312<br />
<br />
;Likelihood-enhanced fast translation functions [http://www.phaser.cimr.cam.ac.uk/images/6/63/Gx5042.pdf pdf]<br />
:McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ<br />
:Acta Cryst. (2005). D61, 458-464<br />
<br />
;Simple algorithm for a maximum-likelihood SAD function [http://scripts.iucr.org/cgi-bin/paper?ea5015 pdf]<br />
:McCoy AJ, Storoni LC, Read RJ<br />
:Acta Cryst. (2004). D60, 1220-1228<br />
<br />
;Likelihood-enhanced fast rotation functions [http://www.phaser.cimr.cam.ac.uk/images/3/3a/Ad5007.pdf pdf]<br />
:Acta Cryst. (2004). D60, 432-438<br />
: Storoni LC, McCoy AJ, Read RJ<br />
<br />
;Pushing the boundaries of molecular replacement with maximum likelihood [http://www.phaser.cimr.cam.ac.uk/images/a/a6/Ba5014r.pdf pdf]<br />
:Read RJ<br />
:Acta Cryst. (2001). D57, 1373-1382</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=1518Keywords2012-06-27T16:52:07Z<p>WikiSysop: /* link=NMADOMAIN */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
'''These keywords are for the current (nightly build) release of Phaser through [http://www.phenix-online.org/download/ Phenix] .'''<br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <FILENAME>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> PDB <PDBFILE> [RMS <RMS><sup>1</sup>|IDENTITY <ID><sup>2</sup>|CARD ON<sup>3</sup>] ''{PDB <PDBFILE> [RMS <RMS>|IDENTITY <ID>|CARD ON] }…''<br />
: The names of the PDB files used to build the ENSEMBLE, and either<br />
: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW><br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms.<br />
; ENSEMBLE <MODLID> FRACTION <FRAC_SCAT><br />
: Fraction scattering of ensemble entered directly rather than calculated from composition<br />
;[[Image:Expert.gif|24px]] ENSEMBLE <MODLID> BINS MIN <L> MAX <H> WIDTH <W> CUBIC <A> <nowiki><B></nowiki> <C><br />
: Bins for the calculated data for MODLID (in P1 cell). See [[#BINS | BINS]] for details of sub-keywords.<br />
;[[Image:Expert.gif|24px]] ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
* Default: ENSEMBLE <MODLID> BINS MIN 5 MAX 200 WIDTH 1000 CUBIC 0 1 0<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
setENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>)<br />
setENSE_BINS_MIN(str <MODLID>,float <L>)<br />
setENSE_BINS_MAX(str <MODLID>,float <H>)<br />
setENSE_BINS_WIDTH(str <MODLID>,float <W>)<br />
setENSE_BINS_CUBIC(str <MODLID>,dvect3 <A> <nowiki><B></nowiki> <C>)<br />
setENSE_FRAC(str <MODLID>,float <FRAC_SCAT>)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF><br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
setLABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | NMA | NCS | MR_AUTO | MR_FRF | MR_FTF | MR_BRF | MR_BTF | MR_RNP | MR_LLG | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runNMA(InputNMA)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR_RF r = runMR_BRF(InputMR_BRF)<br />
ResultMR_TF r = runMR_BTF(InputMR_BTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultMR r = runMR_LLG(InputMR_LLG)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for SAD refinement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for SAD refinement.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the "full search" or "fast search" algorithms.<br />
; SEARCH DEEP [ON|OFF]<br />
: Search method FAST only. Flag to control whether or not the cuttoff for the peaks in the rotation function is reduced if there is no TFZ over ZSCORE_CUTOFF in the first search.<br />
; SEARCH DOWN PERCENT <PERC><br />
: Search method FAST only. Percentage to reduce rotation function cutoff if there is no TFZ over ZSCORE_CUTOFF in first search.<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH DEEP ON<br />
* Default: SEARCH DOWN PERCENT 25<br />
* Default: SEARCH BFACTOR 0<br />
addSEAR_ENSE_NUMB(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUMB(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_ORDE_AUTO(bool])<br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_DOWN_PERC(float <PERC>)<br />
setSEAR_BFAC(float <BFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
; SGALTERNATIVE SORT [ON|OFF]<br />
: Sort alternative space group list in order of frequency of occurrence.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
* Default: SGALTERNATIVE SORT ON<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
setSGAL_SORT(bool)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched).<br />
; SOLUTION ENSEMBLE <MODLID> VRMS <V1> <V2> ...<br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION SOLPAR FSOL <FSOL><br />
; SOLUTION SOLPAR BSOL <BSOL><br />
; SOLUTION SOLPAR FIXB <FIXB><br />
: Solvent parameters for the solution (if refined). See [[#SOLPARAMETERS | SOLPARAMETERS]] keyword for details.<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>) <br />
setSOLU_SPAC(str <SG>)<br />
addSOLU_ENSE_VRMS(str <MODLID>, float_array <VARIANCES>) <br />
setSOLU_SOLP_FSOL(float)<br />
setSOLU_SOLP_BSOL(float)<br />
setSOLU_SOLP_FIXB(bool)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the atomic Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical (or default) input for keyword NMAMethod. Use WRITe to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool) <br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]''<br />
: Toggle for output coordinate files. If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
; ELLG USE [ON|OFF]<br />
: Use expected LLG to determine resolution limits and search order<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
* Default: ELLG USE ON<br />
* Default: ELLG TARGET 120<br />
setELLG_USE(bool <True|False>)<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the given hand of heavy atoms <br />
: <sup>2</sup>Phase using other hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGComplete COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGComplete SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGComplete CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGComplete SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGComplete NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGComplete MAPS [ON|OFF]<br />
: Output map coefficients to mtz file<br />
; LLGComplete METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete MAPS OFF<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_MAPS(bool <True|False>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMADOMAIN== <br />
; NMADOMAIN ENABLE [ON| OFF] <br />
: Use NMA to determine domain structure of protein rather than using it to perturb a pdb file<br />
; NMADOMAIN NUMBER <NUMB><br />
:Number of domains into which to split the protein<br />
; NMADOMAIN EQUALITY [ON| OFF] <br />
: Use the Equality Test to score positions of domain boundaries. Boundaries that divide the protein more equally score more highly.<br />
; NMADOMAIN SPHERICITY [ON| OFF] <br />
: Use the Sphericity Test to score positions of domain boundaries. Boundaries that divide the protein into more spherical domains score more highly.<br />
; NMADOMAIN DENSITY [ON| OFF] <br />
: Use the Density Test to score positions of domain boundaries. Boundaries that divide the protein into domains more densely packed with atoms score more highly.<br />
; NMADOMAIN CONTINUITY [ON| OFF] <br />
: Use the Continuity Test to score positions of domain boundaries. Boundaries that divide the protein into domains contigous in sequence score more highly.<br />
; NMADOMAIN WEIGHT EQUALITY <WEIGHT><br />
: Weight factor for the the Equality Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT SPHERICITY <WEIGHT><br />
: Weight factor for the the Density Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT DENSITY <WEIGHT><br />
: Weight factor for the the Equality Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT CONTINUITY <WEIGHT><br />
: Weight factor for the the Continuity Test in the total Domain Score.<br />
; NMADOMAIN DDM SLIDER <VAL><br />
; NMADOMAIN DDM STEP <VAL><br />
; NMADOMAIN DDM MIN <VAL><br />
; NMADOMAIN DDM MAX <VAL><br />
: Difference Distance Matrix parameters. The SLIDER window width is used to smooth the DDM. The STEP is the fraction of the difference between the lowest and highest DDM values used to step (from MIN to MAX) though in search of optimal Domain Score.<br />
; NMADOMAIN DISTANCE MIN <VAL><br />
; NMADOMAIN DISTANCE MAX <VAL><br />
: Difference Distance Matrix parameters. The DISTANCE (from MIN to MAX) in Angstroms used in search of optimal Domain Score.<br />
; NMADOMAIN SEQUENCE MIN <VAL><br />
; NMADOMAIN SEQUENCE MAX <VAL><br />
: Difference Distance Matrix parameters. The SEQUENCE separation between matrix pairs (from MIN to MAX)used in search of optimal Domain Score.<br />
; NMADOMAIN JOIN MIN <VAL><br />
; NMADOMAIN JOIN MAX <VAL><br />
: Difference Distance Matrix parameters. The lengths of the sequences to JOIN (from MIN to MAX) if domain segments are discontinuous in search of optimal Domain Score.<br />
* Default: NMADOMAIN ENABLE OFF<br />
* Default: NMADOMAIN NUMBER 2<br />
* Default: NMADOMAIN EQUALITY ON<br />
* Default: NMADOMAIN SPHERICITY ON <br />
* Default: NMADOMAIN DENSITY ON<br />
* Default: NMADOMAIN CONTINUITY OFF<br />
* Default: NMADOMAIN WEIGHT EQUALITY 1<br />
* Default: NMADOMAIN WEIGHT SPHERICITY 4 <br />
* Default: NMADOMAIN WEIGHT DENSITY 1<br />
* Default: NMADOMAIN WEIGHT CONTINUITY 1<br />
* Default: NMADOMAIN DDM SLIDER 0<br />
* Default: NMADOMAIN DDM STEP 50<br />
* Default: NMADOMAIN DDM MIN 1<br />
* Default: NMADOMAIN DDM MAX 5<br />
* Default: NMADOMAIN JOIN MIN -1<br />
* Default: NMADOMAIN JOIN MAX -1<br />
* Default: NMADOMAIN SEQUENCE MIN 0<br />
* Default: NMADOMAIN SEQUENCE MAX 1<br />
* Default: NMADOMAIN DISTANCE MIN 7<br />
* Default: NMADOMAIN DISTANCE MAX 14<br />
setNMAD_ENAB(bool)<br />
addNMAD_NUMB(int <NUMB>) <br />
setNMAD_EQUA(bool)<br />
setNMAD_SPHE(bool)<br />
setNMAD_DENS(bool)<br />
setNMAD_CONT(bool)<br />
setNMAD_WEIG_EQUA(float <WEIGHT>) <br />
setNMAD_WEIG_SPHE(float <WEIGHT>) <br />
setNMAD_WEIG_DENS(float <WEIGHT>)<br />
setNMAD_WEIG_CONT(float <WEIGHT>)<br />
setNMAD_DDM_SLID(int <VAL>) <br />
setNMAD_DDM_STEP(int <VAL>) <br />
setNMAD_DDM_MINI(int <VAL>) <br />
setNMAD_DDM_MAXI(int <VAL>) <br />
setNMAD_JOIN_MINI(int <VAL>) <br />
setNMAD_JOIN_MAXI(int <VAL>) <br />
setNMAD_SEQU_MINI(int <VAL>) <br />
setNMAD_SEQU_MAXI(int <VAL>) <br />
setNMAD_DIST_MINI(float <VAL>) <br />
setNMAD_DIST_MAXI(float <VAL>)<br />
<br />
==[[Image:User2.gif|link=]]NMAPDB== <br />
; NMAPDB PERTURB [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; NMAPDB MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. <br />
; NMAPDB COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
; NMAPDB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; NMAPDB RMS CLASH <CLASH> <br />
; NMAPDB RMS STRETCH <STRETCH> <br />
; NMAPDB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until either the C-alpha atoms clash with (come within CLASH Ångstroms of) other C-alpha atoms, the distances between C-alpha atoms STRETCH too far (note that normal modes do not preserve the geometry) or the MAXRMS deviation has been reached.<br />
; NMAPDB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; NMAPDB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: NMAPDB MODE 7 <br />
* Default: NMAPDB COMBINATION 3<br />
* Default: NMAPDB PERTURB RMS <br />
* Default: NMAPDB RMS STEP 0.3 <br />
* Default: NMAPDB RMS STRETCH 5.0 <br />
* Default: NMAPDB RMS CLASH 2.0<br />
* Default: NMAPDB RMS MAXRMS 0.5<br />
* Default: NMAPDB RMS DIRECTION TOFRO<br />
setNMAP_PERT(str [ "RMS" | "DQ" ])<br />
addNMAP_MODE(int <MODE>) <br />
setNMAP_COMB(int <NMAX>)<br />
setNMAP_RMS_CLAS(float <CLASH>) <br />
setNMAP_RMS_STRE(float <STRETCH>) <br />
setNMAP_RMS_MAXI(float <MAX>)<br />
setNMAP_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addNMAP_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>BEST | <sup>2</sup>ALLOW | <sup>3</sup>PERCENT | <sup>4</sup>ALL ]<br />
: <sup>1</sup>Allow the best packing solutions only, provided the total number of clashes does not exceed ALLOWED_CLASHES<br />
: <sup>2</sup>Allow all solutions that pack with number of C-alpha clashes less than ALLOWED_CLASHES<br />
: <sup>3</sup>Allow up to the ALLOWED_CLASHES percentage of C-alpha atoms of the model structure to clash<br />
: <sup>4</sup>Allow all solutions (no packing test)<br />
: If the model is RNA or DNA, phosphate (P) and carbon atoms (C3* and C4*) in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes. The atom names must start in column 14 (leaving one space at the beginning of the field), and the residue names must be right-justified (i.e. in column 20 for the single-letter names of ribonucleotides such as A, or in columns 19-20 for the two letter names of deoxyribonucleotides such as DA).<br />
; PACK CUTOFF <ALLOWED_CLASHES> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (ZSCORE keyword).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
;[[Image:Expert.gif|24px]] PACK DISTANCE <DISTANCE><br />
: Distance within which C-alpha atoms clash given by DISTANCE Ångstroms. If the model is RNA or DNA, phosphate and carbon atoms in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes<br />
;[[Image:Expert.gif|24px]] PACK TRACE [ON|OFF]<br />
: Toggle whether or not to only use Trace atoms (C-alpha atoms in proteins and P in RNA/DNA) for packing analysis, or all atoms. Only recommended to be OFF for use with small fragments.<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK QUICK ON<br />
* Default: PACK COMPACT ON<br />
* Default: PACK DISTANCE 3.0<br />
setPACK_SELE(str ["BEST"|"ALLOW"|"PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_COMP(bool)<br />
setPACK_DIST(float <DISTANCE>)<br />
setPACK_TRAC(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for the rotation function (ROT) or translation function (TRA) satisfying selection criteria are saved<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH MEHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<br />
; PURGE TRA ENABLE [ON|OFF]<br />
: Toggle for whether to purge the solution list from the RF or TF and after the refinement steps (in AUTO mode) according to the best solution found so far.<br />
; PURGE ROT PERCENT <PERC><br />
; PURGE TRA PERCENT <PERC><br />
: PERC is the percent of the difference between the top solution and the mean at which to purge the solutions.<br />
; PURGE ROT NUMBER <NUM><br />
; PURGE TRA NUMBER <NUM><br />
: NUM is the number of solutions to retain in purging. The number taken is the minimum of the number found with the PERCENT cutoff and the NUMBER cutoff. If NUM is zero then the number is not used as a selection criteria.<br />
* Default: PURGE ROT ENABLE ON PERC 75 NUM 0<br />
* Default: PURGE TRA ENABLE ON PERC 75 NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
; RESOLUTION AUTO LOW <LORES> <br />
: Low resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO_AUTO_LOW(float <LORES>)<br />
setRESO(float <HIRES>,float <LORES>) <br />
setRESO_AUTO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
* Default: ROTATE VOLUME FULL<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS REFINE ROTATION [ON | OFF]<br />
: Use TNCS correction method that includes a rotation refinement of the two TNCS related rotations (to separate the rotation function results) before the translation function<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes (GRID OFF). Central value for grid search (GRID ON).<br />
; TNCS ROTATION GRID [ON | OFF]<br />
: Refine the initial rotation angle starting from a grid of orientations around the starting angle (default 0,0,0). Grid controlled by RANGE and SAMPLING. The best refined rotational angle will be selected.<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minium distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS USE ON<br />
* Default: TNCS REFINE ROTATION OFF<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION GRID ON<br />
* Default: TNCS ROTATION SAMPLING 0<br />
* Default: TNCS ROTATION RANGE 0<br />
* Default: TNCS VARIANCE RMS 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15<br />
* Default: TNCS NMOL 2<br />
setTNCS_USE(bool)<br />
setTNCS_REFI_ROTA(bool)<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>)<br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>) <br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_NMOL(int <NMOL>)<br />
<br />
==[[Image:User2.gif|link=]]TRANSLATE== <br />
; TRANSLATE VOLUME [ <sup>1</sup>FULL| <sup>2</sup>REGION| <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search along line. <br />
: <sup>3</sup> Search region.<br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATE START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATE END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATE POINT <X Y Z><br />
; <sup>4</sup>TRANSLATE RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATE [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
* Default: TRANSLATE VOLUME FULL<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with SEARCH METHOD FAST. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
==[[Image:Expert.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''SOLP [ON|OFF] LAST [ON|OFF} NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACMR PROTOCOL DEFAULT<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <SOLP>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD K [ON|OFF] B [ON|OFF] SIGMA [ON|OFF] XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(bool <K>,bool <nowiki><B></nowiki>,bool <SIGMA>,<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]NMAMETHOD== <br />
; NMAMETHOD OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>CA | <sup>3</sup>ALL ] <br />
: Define the atoms used for the normal mode analysis. <br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use C-alpha atoms only to determine the modes.<br />
: <sup>3</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; NMAMETHOD MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; NMAMETHOD NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; NMAMETHOD RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; NMAMETHOD FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: NMAMETHOD OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setNMAM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setNMAM_RTB_MAXB(float <MAXB>)<br />
setNMAM_RTB_NRES(float <NRES>) <br />
setNMAM_RADI(float <RADIUS>) <br />
setNMAM_FORC(float <FORCE>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with search method [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (MODE = MR_BRF or MR_FRF)<br />
* Default: SAMP = dmin/5; (MODE = MR_BTF)<br />
* Default: SAMP = dmin/4; (MODE = MR_FTF)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS MIN <L> <br />
: The binning of the data. L = minimum number of bins.<br />
; BINS MAX <H> <br />
: The binning of the data. H = maximum number of bins.<br />
; BINS WIDTH <W><br />
: The binning of the data. W = width of the bins in number of reflections<br />
; BINS CUBIC <A> <nowiki><B></nowiki> <C><br />
: The binning of the data. A B C are the coefficients for the binning function A(S*S*S)+B(S*S)+CS where S = (1/resolution). Cubic coefficients restricted to monotonically increasing function: A >0, B >0, C >0 and either (a) A=B=0 or (b) A=0 or (c) B=0<br />
* Default: BINS MIN 6 MAX 50 WIDTH 500 CUBIC 0 1 0 <br />
setBINS_MINI(float <L>)<br />
setBINS_MAXI(float <H>)<br />
setBINS_WIDT(float <W>)<br />
setBINS_CUBI(dvect3 <A B C>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for molecular Bfactor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 10<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; CELL <A> <nowiki><B></nowiki> <C> <ALPHA> <BETA> <GAMMA><br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]CLMN== <br />
; CLMN SPHERE <SPHERE><br />
: Radius for the decomposition of the Patterson in Ångstroms. If it is 0, the radius defaults to twice the mean radius of the ENSEMBLE.<br />
; CLMN LMIN <LMIN><br />
: Lower limit of L values.<br />
; CLMN LMAX <LMAX><br />
: Upper limit of L values. The largest L value used in the calculation is the minimum of LMAX and 2&pi; * SPHERE/dmin.<br />
* Default: CLMN LMIN 4<br />
* Default: CLMN LMAX 100<br />
* Default: CLMN SPHE 0<br />
setCLMN_SPHE(float <SPHERE>) <br />
setCLMN_LMIN(float <LMIN>) <br />
setCLMN_LMAX(float <LMAX>)<br />
<br />
==[[Image:Developer.gif|link=]]FFTS==<br />
; FFTS MIN <ATOMS_MIN> MAX <ATOMS_MAX><br />
: The minimum and maximum number of atoms of the range between which direct summation and fft methods are tested to see which is faster for structure factor and gradient calcuation (for this unit cell and resolution). For a number of atoms below ATOMS_MIN direct structure factor calculation is always used, and for a number of atoms above ATOMS_MAX ffts are always used for the structure factor calculation and the gradient calculations. Direct summation is always used for the curvatures. Use FFTS MIN 0 MAX O to always use ffts.<br />
* Default: FFTS MIN 20 MAX 80<br />
setFFTS_MINI(float <ATOMS_MIN>) <br />
setFFTS_MAXI(float <ATOMS_MAX>)<br />
<br />
==[[Image:Developer.gif|link=]]INTEGRATION==<br />
; INTEGRATION FIXED [ON|OFF]<br />
: Fix the number of integration points or determine the number of angular steps in the integration by the variance of the function<br />
; INTEGRATION STEP <STEP><br />
: Number of steps in angular integration of function if FIXED number of points<br />
* Default: INTEGRATION FIXED OFF<br />
setINTE_FIXE(bool <True|False>) <br />
setINTE_STEP(float <STEP>)<br />
<br />
==[[Image:Developer.gif|link=]]MACHL== <br />
; MACHL PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of Hendrickson-Lattman coefficients<br />
; MACHL COEF [ON|OFF] ''NCYCle <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of Hendrickson-Lattman coefficients. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACHL PROTOCOL DEFAULT<br />
setMACH_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACH(bool <COEF>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
;NORMALIZATION BINS <B1 B2 ...> ANISO <HH> <KK> <LL> <HK> <HL> <KL> SOLK <SOLK> SOLB <SOLB><br />
: The normalization factors that correct for anisotropy in the data<br />
setNORM_BINS(float_array <B1 B2 ...>)<br />
setNORM_ANIS(dmat6 <HH KK LL HK HL KL>)<br />
setNORM_SOLK(float <SOLK>) <br />
setNORM_SOLB(float <SOLB>) <br />
setNORM(float_array <B1 B2 ...> ,dmat6 <HH KK LL HK HL KL>,float <SOLK>,float <SOLB>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS FSOL <FSOL> BSOL <BSOL> FIXB [ON|OFF]<br />
: Babinet solvent parameters for Sigma(A) curves. If FIXB is OFF, then BSOL is calculated from FSOL using the formula BSOL = 99.1 + 5.79*exp(4.03*FSOL) from Glykos & Kokkinkdis Acta Cryst D56 p1070 (2000), otherwise BSOL is fixed at the input (or default) value.<br />
; SOLPARAMETERS RESTRAIN [ON|OFF]<br />
: Restrain the Babinet solvent parameters to the initial values during refinement.<br />
; SOLPARAMETERS RESOLUTION <HIRES><br />
; Do not apply Babinet solvent correction terms to resolutions higher than HIRES.<br />
* Default: SOLPARAMETERS FSOL 0.69 BSOL 378 FIXB ON<br />
* Default: SOLPARAMETERS RESTRAINT OFF<br />
* Default: SOLPARAMETERS RESOLUTION 0<br />
setSOLP_FSOL(float <FSOL>) <br />
setSOLP_BSOL(float <BSOL>)<br />
setSOLP_FIXB(bool) <br />
setSOLP_REST(bool)<br />
<br />
==[[Image:Developer.gif|link=]]SORT==<br />
; SORT [ON|OFF]<br />
: Sort the reflections into resolution order upon reading MTZ file, for performance gain in molecular replacement<br />
* Default: SORT ON<br />
setSORT(bool)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET==<br />
; TARGET FRF [LERF1|LERF2|CROWTHER]<br />
: Target function for fast rotation searches (2)<br />
; TARGET FTF [LETF1|LETF2|CORRELATION]<br />
: Target function for fast translation searches (3)<br />
* Default: TARGET FRF LERF1 <br />
* Default: TARGET FTF LETF1<br />
setTARG_FRF(str ["LERF1"|"LERF2"|"CROWTHER"])<br />
setTARG_FTF(str ["LETF1"|"LETF2"|"CORRELATION"])<br />
<br />
==[[Image:Developer.gif|link=]]VARSAD==<br />
; VARSAD [ K <N> | B <N> | SIGMA <N> | SA <B1 B2 …> | SB <B1 B2 …> | SP <B1 B2 …> | SD <B1 B2 …> | PK <N> | PB <N>]<br />
: SAD variance parameters SA and SB (the real and imaginary components of Sigma Minus), SP (Sigma Plus) and SD (Sigma Delta) by resolution bin, the overall scale (K) and B-factor (B) for the anomalous scatterer model, the overall scale (PK) and B-factor (PB) for the partial structure (if given), and sigma-scale (SIGMA).<br />
setVARS(float_array <VARIANCES></div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Releases&diff=1517Releases2012-06-27T16:43:48Z<p>WikiSysop: /* 2012 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==2012==<br />
; 27th June 2012 - date (active development)<br />
: '''Phaser-2.5.1 released with Phenix nightly builds'''<br />
:*Features of Phaser-2.5.1<br />
::*'''Domain Analysis''' NMA used to identify domains in proteins<br />
<br />
; 23rd June 2012 <br />
: '''Phaser-2.5.0 released with Phenix-1.8'''<br />
<br />
; 24th April 2012<br />
:Major update of Phaserwiki to reflect powerful new Phaser functionality (Phaser-2.5.0)<br />
<br />
; 23rd December 2011 - date (active development)<br />
: '''Phaser-2.5.0 released with Phenix nightly builds'''<br />
:*Features of Phaser-2.5.0<br />
::*Wiki '''documentation''' (using ''wikidump'') distributed with source code<br />
::*'''Expected LLG''' used to optimize search strategy in FAST mode<br />
::*Babinet '''sovent correction''' terms can be refined.<br />
::*'''Single Atom MR''' enabled. Phaser ensembles can be single atoms. Suitable for high resolution data (better than 1.2A) only.<br />
::*Cumulative Intensity statistics (loggraphs) printed before and after anisotropy and tNCS correction to aid '''twinning detection'''<br />
::*'''Translational NCS correction''' terms applied by default. Phaser 2.5.0 gives much higher signal-to-noise for molecular replacement solutions and SAD LLG maps where the crystal has pseudo-translational NCS (including pseudo-centring) (c.f. previous versions). (23-12-11)<br />
::*'''CCP4 GUI interface''' (ccp4i) files (for directories tasks, templates and scripts) now distributed with phaser source code (phaser svn). Copy (or link) files to ccp4i installation (in directories tasks, templates and scripts) to synchronise phaser source code/executable with ccp4i (23-12-11)<br />
<br />
==2011==<br />
<br />
; 8th December 2011 - 23rd December 2011<br />
: '''Phaser-2.4.1 released with Phenix nightly builds'''<br />
:*Features of Phaser-2.4.1<br />
::*Heterogen atoms carried through in PDB file in MR and not deleted (scattering not used, as before) (8-12-11)<br />
::*Bugfix for problem with packing function accepting cases where an ensemble with internal point group symmetry is on a special position<br />
<br />
; 7th December 2011<br />
: '''Phaser-2.4 released with Phenix-1.7.3'''<br />
:*Features of Phaser-2.4<br />
::*Pseudo-translational NCS correction for MR and SAD phasing available, but not default (25-11-11)<br />
::*FAST search method turned on by default, replacing FULL search method default (17-11-11)<br />
::*MR possible with a model containing a flat molecule or single atom, for extending a MR solution to add flat ligands or metal ions (17-11-11)<br />
::*B-factor refinement turned on by default in molecular replacement (2-11-11)<br />
::*Bugfix for occasional and irreproducible segmentation faults for 32 bit binary running on 64 bit Linux<br />
::*Packing function accepts cases where an ensemble with internal point group symmetry is on a special position, and pdb file output deletes atoms overlapped due to the symmetry of special position<br />
<br />
; 15th July 2011<br />
: '''Phaser-2.3 released with CCP4-6.2.0'''<br />
<br />
==2010==<br />
; 16th December 2010<br />
: '''Phaser-2.3 released with Phenix'''<br />
:*Features of Phaser-2.3<br />
::*Option to refine variance of an ensemble ("RMS deviation" of target to model) <br />
::*Option for "FAST" search method that finds multiple copies of same ensemble more efficiently<br />
::*Significant speed up of fast rotation function<br />
::*Significant speed up of rigid body refinement (analytic gradients and hessian, rather than finite differences)<br />
::*Packing function - number of allowed clashes scales with the size of the molecules (percentage of atoms)<br />
::*Loggraphs of FOM vs resolution<br />
::*Option to give electron density as a model for SAD phasing<br />
<br />
==2009==<br />
<br />
; 1st October 2009<br />
: '''Phaser-2.2 released'''<br />
:* New features Phaser-2.2<br />
:**Reduced memory requirements<br />
:**For anisotropic data, map coefficients sharpened to falloff of strongest direction<br />
:**Improvements to SAD log-likelihood-gradient substructure completion<br />
:**Automated reassignment of atom types, when more than one type of scatterer<br />
:**Improved sensitivity of LLG completion protocol<br />
:**Facility to compare MR solutions with prior ("template") solution, e.g. from another program<br />
:**Refine relative B-factors of different components of MR solution<br />
:**Recognize internal symmetry in MR model, use to identify equivalent solutions<br />
:**Updated atom names consistent with PDBv3<br />
<br />
==2008==<br />
<br />
; 14th January 2008<br />
: '''Phaser-2.1.2 released'''<br />
:* Download from this website and with phenix-1.3b<br />
:* Patch to fix segmentation fault in non-linux executables<br />
<br />
==2007==<br />
<br />
; 12th December 2007<br />
: '''CCP4 Automated Downloads'''<br />
: A Phaser module is now available through the CCP4 automated Downloads page and from the Daresbury ftp server.<br />
<br />
; 12th November 2007<br />
: '''Phaser-2.1.1 released'''<br />
:* New Features Phaser-2.1.1<br />
:** Default packing criteria relaxed to allow a small number of clashes<br />
:** Default packing distance increased to identify intercalation of helices<br />
:** Composition can be estimated from solvent content<br />
:** Default composition corresponds to 50% solvent<br />
:** If automated MR search finds some, but not all, components, the partial solution is output<br />
:** Improved SAD phasing<br />
:** SAD phasing starting from MR partial model<br />
:** Output of PDB hybrid-36 atom numbers and col(21-22) chainids for largest structures<br />
<br />
==2006==<br />
<br />
; 1st November 2006<br />
: '''Phaser-1.3.3 released'''<br />
:* Download with ccp4 6.0.2.<br />
:* New Features Phaser-1.3,3<br />
:**Filename parsing accepts quoted strings, for Windows filenames that include spaces. Change synchronised with corresponding changes throughout the rest of the CCP4 suite.<br />
<br />
;1st July 2006<br />
:'''Phaser-2.0 released'''<br />
:* Download with phenix-1.24-beta<br />
:* Minor Bug fixes from Phaser–1.3<br />
<br />
;1st February 2006<br />
:'''Phaser-1.3.2 released'''<br />
:* Download with ccp4 6.0.0.<br />
:* Minor Bug fixes from Phaser–1.3.1<br />
<br />
==2005==<br />
<br />
; 1st July 2005<br />
: '''Phaser-1.3.1 released'''<br />
:* New Features Phaser-1.3.1<br />
:** Minor bug fixes after Phenix-1.1a release<br />
:** R-factor reported by MR_RNP and MR_LLG modes (verbose output)<br />
<br />
;15th June 2005<br />
: '''Phaser 1.3 released'''<br />
:* Download with Phenix-1.1a<br />
:* New Features Phaser-1.3<br />
:** Release with Phenix-1.1a<br />
:** New Normal Mode Analysis of structures<br />
:** New Cell Content Analysis Mode<br />
:** Improved Automated MR<br />
:** Map coefficients appended to input mtz file<br />
:** Score stored in .sol file is Z-score rather than LLG<br />
:** Final phasing and refinement to full resolution on mtz file<br />
:** Packing of RNA/DNA<br />
:** Packing to form close packed oligomeric complexes<br />
:** Waters in pdb files excluded from packing<br />
:** Only the most similar model in an ensemble is used for packing analysis<br />
:** Reduced memory requirements<br />
:** Composition/MW determined from sequence<br />
:** Automated MR now available as a python script<br />
<br />
;1st June 2005<br />
: '''Phaser-1.2 expired'''<br />
:* A typo in the expiry date in the source code caused the source to expire. A message explaining what happened and possible ways to work around it has been sent to all registered Phaser users. We apologise for the inconvenience, and we are working hard to get version 1.3 (which will not have an expiry date!) released as soon as possible.<br />
<br />
==2004==<br />
<br />
;15th December 2004<br />
:* '''Congratulations to Richard Bunker, who registered as our 1000th user!'''<br />
<br />
; 30th June 2004<br />
: '''Documentation updated'''<br />
:* The README files for the installer, CCP4I GUI installation and the CCP4-4.2 extras have been clarified. Thanks for your feedback.<br />
<br />
; 25th June 2004<br />
: '''Phaser-1.2 released'''<br />
:* Download from here.<br />
:* New Features Phaser-1.2<br />
:** Automated solution of structures<br />
:** New Likelihood Enhanced fast Translation Function (LETF)<br />
:** Ability to use electron density maps as molecular replacement models<br />
:** Rigid body solution refinement against maximum likelihood target<br />
:** Pruning of duplicate solutions from solution list<br />
:** Searching of multiple alternative space groups<br />
:** Searching of multiple alternative models<br />
:** Better minimizers<br />
<br />
==2003==<br />
<br />
; 22nd December 2003<br />
: '''Phaser-cambridge-alpha-1-1a released'''<br />
:* Phaser-cambridge-alpha-1-1 will stop working on the 1st of January 2004. We have therefore released a new version cambridge-alpha-1.1a that will work for another six months. This version is identical in all other areas to 1.1. We are currently working on a new and improved version (1.2) that will be released soon.<br />
<br />
; 4th November 2003<br />
: ''' Documentation online'''<br />
<br />
;26th September 2003<br />
: ''' Phaser-cambridge-alpha-1-1 released'''<br />
:* Bugfix in the anisotropy correction.<br />
<br />
; 6th September 2003<br />
: ''' Phaser-cambridge-alpha-1-0 released'''<br />
<br />
;3rd September 2003<br />
: '''Phaser logo launched'''<br />
<br />
; 28th July 2003<br />
: '''Phaser helpdesk launched''' <br />
:* Contact us on cimr-phaser@lists.cam.ac.uk<br />
<br />
; 14th April 2003<br />
: '''Phaser webpage launched'''</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Releases&diff=1516Releases2012-06-27T16:42:16Z<p>WikiSysop: /* 2012 */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
==2012==<br />
; 23rd June 2012 <br />
: '''Phaser-2.5.0 released with Phenix-1.8'''<br />
<br />
; 24th April 2012<br />
:Major update of Phaserwiki to reflect powerful new Phaser functionality (Phaser-2.5.0)<br />
<br />
; 23rd December 2011 - date (active development)<br />
: '''Phaser-2.5.0 released with Phenix nightly builds'''<br />
:*Features of Phaser-2.5.0<br />
::*Wiki '''documentation''' (using ''wikidump'') distributed with source code<br />
::*'''Expected LLG''' used to optimize search strategy in FAST mode<br />
::*Babinet '''sovent correction''' terms can be refined.<br />
::*'''Single Atom MR''' enabled. Phaser ensembles can be single atoms. Suitable for high resolution data (better than 1.2A) only.<br />
::*Cumulative Intensity statistics (loggraphs) printed before and after anisotropy and tNCS correction to aid '''twinning detection'''<br />
::*'''Translational NCS correction''' terms applied by default. Phaser 2.5.0 gives much higher signal-to-noise for molecular replacement solutions and SAD LLG maps where the crystal has pseudo-translational NCS (including pseudo-centring) (c.f. previous versions). (23-12-11)<br />
::*'''CCP4 GUI interface''' (ccp4i) files (for directories tasks, templates and scripts) now distributed with phaser source code (phaser svn). Copy (or link) files to ccp4i installation (in directories tasks, templates and scripts) to synchronise phaser source code/executable with ccp4i (23-12-11)<br />
<br />
==2011==<br />
<br />
; 8th December 2011 - 23rd December 2011<br />
: '''Phaser-2.4.1 released with Phenix nightly builds'''<br />
:*Features of Phaser-2.4.1<br />
::*Heterogen atoms carried through in PDB file in MR and not deleted (scattering not used, as before) (8-12-11)<br />
::*Bugfix for problem with packing function accepting cases where an ensemble with internal point group symmetry is on a special position<br />
<br />
; 7th December 2011<br />
: '''Phaser-2.4 released with Phenix-1.7.3'''<br />
:*Features of Phaser-2.4<br />
::*Pseudo-translational NCS correction for MR and SAD phasing available, but not default (25-11-11)<br />
::*FAST search method turned on by default, replacing FULL search method default (17-11-11)<br />
::*MR possible with a model containing a flat molecule or single atom, for extending a MR solution to add flat ligands or metal ions (17-11-11)<br />
::*B-factor refinement turned on by default in molecular replacement (2-11-11)<br />
::*Bugfix for occasional and irreproducible segmentation faults for 32 bit binary running on 64 bit Linux<br />
::*Packing function accepts cases where an ensemble with internal point group symmetry is on a special position, and pdb file output deletes atoms overlapped due to the symmetry of special position<br />
<br />
; 15th July 2011<br />
: '''Phaser-2.3 released with CCP4-6.2.0'''<br />
<br />
==2010==<br />
; 16th December 2010<br />
: '''Phaser-2.3 released with Phenix'''<br />
:*Features of Phaser-2.3<br />
::*Option to refine variance of an ensemble ("RMS deviation" of target to model) <br />
::*Option for "FAST" search method that finds multiple copies of same ensemble more efficiently<br />
::*Significant speed up of fast rotation function<br />
::*Significant speed up of rigid body refinement (analytic gradients and hessian, rather than finite differences)<br />
::*Packing function - number of allowed clashes scales with the size of the molecules (percentage of atoms)<br />
::*Loggraphs of FOM vs resolution<br />
::*Option to give electron density as a model for SAD phasing<br />
<br />
==2009==<br />
<br />
; 1st October 2009<br />
: '''Phaser-2.2 released'''<br />
:* New features Phaser-2.2<br />
:**Reduced memory requirements<br />
:**For anisotropic data, map coefficients sharpened to falloff of strongest direction<br />
:**Improvements to SAD log-likelihood-gradient substructure completion<br />
:**Automated reassignment of atom types, when more than one type of scatterer<br />
:**Improved sensitivity of LLG completion protocol<br />
:**Facility to compare MR solutions with prior ("template") solution, e.g. from another program<br />
:**Refine relative B-factors of different components of MR solution<br />
:**Recognize internal symmetry in MR model, use to identify equivalent solutions<br />
:**Updated atom names consistent with PDBv3<br />
<br />
==2008==<br />
<br />
; 14th January 2008<br />
: '''Phaser-2.1.2 released'''<br />
:* Download from this website and with phenix-1.3b<br />
:* Patch to fix segmentation fault in non-linux executables<br />
<br />
==2007==<br />
<br />
; 12th December 2007<br />
: '''CCP4 Automated Downloads'''<br />
: A Phaser module is now available through the CCP4 automated Downloads page and from the Daresbury ftp server.<br />
<br />
; 12th November 2007<br />
: '''Phaser-2.1.1 released'''<br />
:* New Features Phaser-2.1.1<br />
:** Default packing criteria relaxed to allow a small number of clashes<br />
:** Default packing distance increased to identify intercalation of helices<br />
:** Composition can be estimated from solvent content<br />
:** Default composition corresponds to 50% solvent<br />
:** If automated MR search finds some, but not all, components, the partial solution is output<br />
:** Improved SAD phasing<br />
:** SAD phasing starting from MR partial model<br />
:** Output of PDB hybrid-36 atom numbers and col(21-22) chainids for largest structures<br />
<br />
==2006==<br />
<br />
; 1st November 2006<br />
: '''Phaser-1.3.3 released'''<br />
:* Download with ccp4 6.0.2.<br />
:* New Features Phaser-1.3,3<br />
:**Filename parsing accepts quoted strings, for Windows filenames that include spaces. Change synchronised with corresponding changes throughout the rest of the CCP4 suite.<br />
<br />
;1st July 2006<br />
:'''Phaser-2.0 released'''<br />
:* Download with phenix-1.24-beta<br />
:* Minor Bug fixes from Phaser–1.3<br />
<br />
;1st February 2006<br />
:'''Phaser-1.3.2 released'''<br />
:* Download with ccp4 6.0.0.<br />
:* Minor Bug fixes from Phaser–1.3.1<br />
<br />
==2005==<br />
<br />
; 1st July 2005<br />
: '''Phaser-1.3.1 released'''<br />
:* New Features Phaser-1.3.1<br />
:** Minor bug fixes after Phenix-1.1a release<br />
:** R-factor reported by MR_RNP and MR_LLG modes (verbose output)<br />
<br />
;15th June 2005<br />
: '''Phaser 1.3 released'''<br />
:* Download with Phenix-1.1a<br />
:* New Features Phaser-1.3<br />
:** Release with Phenix-1.1a<br />
:** New Normal Mode Analysis of structures<br />
:** New Cell Content Analysis Mode<br />
:** Improved Automated MR<br />
:** Map coefficients appended to input mtz file<br />
:** Score stored in .sol file is Z-score rather than LLG<br />
:** Final phasing and refinement to full resolution on mtz file<br />
:** Packing of RNA/DNA<br />
:** Packing to form close packed oligomeric complexes<br />
:** Waters in pdb files excluded from packing<br />
:** Only the most similar model in an ensemble is used for packing analysis<br />
:** Reduced memory requirements<br />
:** Composition/MW determined from sequence<br />
:** Automated MR now available as a python script<br />
<br />
;1st June 2005<br />
: '''Phaser-1.2 expired'''<br />
:* A typo in the expiry date in the source code caused the source to expire. A message explaining what happened and possible ways to work around it has been sent to all registered Phaser users. We apologise for the inconvenience, and we are working hard to get version 1.3 (which will not have an expiry date!) released as soon as possible.<br />
<br />
==2004==<br />
<br />
;15th December 2004<br />
:* '''Congratulations to Richard Bunker, who registered as our 1000th user!'''<br />
<br />
; 30th June 2004<br />
: '''Documentation updated'''<br />
:* The README files for the installer, CCP4I GUI installation and the CCP4-4.2 extras have been clarified. Thanks for your feedback.<br />
<br />
; 25th June 2004<br />
: '''Phaser-1.2 released'''<br />
:* Download from here.<br />
:* New Features Phaser-1.2<br />
:** Automated solution of structures<br />
:** New Likelihood Enhanced fast Translation Function (LETF)<br />
:** Ability to use electron density maps as molecular replacement models<br />
:** Rigid body solution refinement against maximum likelihood target<br />
:** Pruning of duplicate solutions from solution list<br />
:** Searching of multiple alternative space groups<br />
:** Searching of multiple alternative models<br />
:** Better minimizers<br />
<br />
==2003==<br />
<br />
; 22nd December 2003<br />
: '''Phaser-cambridge-alpha-1-1a released'''<br />
:* Phaser-cambridge-alpha-1-1 will stop working on the 1st of January 2004. We have therefore released a new version cambridge-alpha-1.1a that will work for another six months. This version is identical in all other areas to 1.1. We are currently working on a new and improved version (1.2) that will be released soon.<br />
<br />
; 4th November 2003<br />
: ''' Documentation online'''<br />
<br />
;26th September 2003<br />
: ''' Phaser-cambridge-alpha-1-1 released'''<br />
:* Bugfix in the anisotropy correction.<br />
<br />
; 6th September 2003<br />
: ''' Phaser-cambridge-alpha-1-0 released'''<br />
<br />
;3rd September 2003<br />
: '''Phaser logo launched'''<br />
<br />
; 28th July 2003<br />
: '''Phaser helpdesk launched''' <br />
:* Contact us on cimr-phaser@lists.cam.ac.uk<br />
<br />
; 14th April 2003<br />
: '''Phaser webpage launched'''</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=1515Keywords2012-06-27T16:36:36Z<p>WikiSysop: /* link=NMADOMAIN */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
'''These keywords are for the current (nightly build) release of Phaser through [http://www.phenix-online.org/download/ Phenix] .'''<br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
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<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <FILENAME>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> PDB <PDBFILE> [RMS <RMS><sup>1</sup>|IDENTITY <ID><sup>2</sup>|CARD ON<sup>3</sup>] ''{PDB <PDBFILE> [RMS <RMS>|IDENTITY <ID>|CARD ON] }…''<br />
: The names of the PDB files used to build the ENSEMBLE, and either<br />
: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW><br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms.<br />
; ENSEMBLE <MODLID> FRACTION <FRAC_SCAT><br />
: Fraction scattering of ensemble entered directly rather than calculated from composition<br />
;[[Image:Expert.gif|24px]] ENSEMBLE <MODLID> BINS MIN <L> MAX <H> WIDTH <W> CUBIC <A> <nowiki><B></nowiki> <C><br />
: Bins for the calculated data for MODLID (in P1 cell). See [[#BINS | BINS]] for details of sub-keywords.<br />
;[[Image:Expert.gif|24px]] ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
* Default: ENSEMBLE <MODLID> BINS MIN 5 MAX 200 WIDTH 1000 CUBIC 0 1 0<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
setENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>)<br />
setENSE_BINS_MIN(str <MODLID>,float <L>)<br />
setENSE_BINS_MAX(str <MODLID>,float <H>)<br />
setENSE_BINS_WIDTH(str <MODLID>,float <W>)<br />
setENSE_BINS_CUBIC(str <MODLID>,dvect3 <A> <nowiki><B></nowiki> <C>)<br />
setENSE_FRAC(str <MODLID>,float <FRAC_SCAT>)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF><br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
setLABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | NMA | NCS | MR_AUTO | MR_FRF | MR_FTF | MR_BRF | MR_BTF | MR_RNP | MR_LLG | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runNMA(InputNMA)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR_RF r = runMR_BRF(InputMR_BRF)<br />
ResultMR_TF r = runMR_BTF(InputMR_BTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultMR r = runMR_LLG(InputMR_LLG)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for SAD refinement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for SAD refinement.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the "full search" or "fast search" algorithms.<br />
; SEARCH DEEP [ON|OFF]<br />
: Search method FAST only. Flag to control whether or not the cuttoff for the peaks in the rotation function is reduced if there is no TFZ over ZSCORE_CUTOFF in the first search.<br />
; SEARCH DOWN PERCENT <PERC><br />
: Search method FAST only. Percentage to reduce rotation function cutoff if there is no TFZ over ZSCORE_CUTOFF in first search.<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH DEEP ON<br />
* Default: SEARCH DOWN PERCENT 25<br />
* Default: SEARCH BFACTOR 0<br />
addSEAR_ENSE_NUMB(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUMB(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_ORDE_AUTO(bool])<br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_DOWN_PERC(float <PERC>)<br />
setSEAR_BFAC(float <BFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
; SGALTERNATIVE SORT [ON|OFF]<br />
: Sort alternative space group list in order of frequency of occurrence.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
* Default: SGALTERNATIVE SORT ON<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
setSGAL_SORT(bool)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched).<br />
; SOLUTION ENSEMBLE <MODLID> VRMS <V1> <V2> ...<br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION SOLPAR FSOL <FSOL><br />
; SOLUTION SOLPAR BSOL <BSOL><br />
; SOLUTION SOLPAR FIXB <FIXB><br />
: Solvent parameters for the solution (if refined). See [[#SOLPARAMETERS | SOLPARAMETERS]] keyword for details.<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>) <br />
setSOLU_SPAC(str <SG>)<br />
addSOLU_ENSE_VRMS(str <MODLID>, float_array <VARIANCES>) <br />
setSOLU_SOLP_FSOL(float)<br />
setSOLU_SOLP_BSOL(float)<br />
setSOLU_SOLP_FIXB(bool)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the atomic Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical (or default) input for keyword NMAMethod. Use WRITe to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool) <br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]''<br />
: Toggle for output coordinate files. If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
; ELLG USE [ON|OFF]<br />
: Use expected LLG to determine resolution limits and search order<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
* Default: ELLG USE ON<br />
* Default: ELLG TARGET 120<br />
setELLG_USE(bool <True|False>)<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the given hand of heavy atoms <br />
: <sup>2</sup>Phase using other hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGComplete COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGComplete SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGComplete CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGComplete SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGComplete NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGComplete MAPS [ON|OFF]<br />
: Output map coefficients to mtz file<br />
; LLGComplete METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete MAPS OFF<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_MAPS(bool <True|False>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMADOMAIN== <br />
; NMADOMAIN ENABLE [ON| OFF] <br />
: Use NMA to determine domain structure of protein rather than using it to perturb a pdb file<br />
; NMADOMAIN NUMBER <NUMB><br />
:Number of domains into which to split the protein<br />
; NMADOMAIN EQUALITY [ON| OFF] <br />
: Use the Equality Test to score positions of domain boundaries. Boundaries that divide the protein more equally score more highly.<br />
; NMADOMAIN SPHERICITY [ON| OFF] <br />
: Use the Sphericity Test to score positions of domain boundaries. Boundaries that divide the protein into more spherical domains score more highly.<br />
; NMADOMAIN DENSITY [ON| OFF] <br />
: Use the Density Test to score positions of domain boundaries. Boundaries that divide the protein into domains more densely packed with atoms score more highly.<br />
; NMADOMAIN CONTINUITY [ON| OFF] <br />
: Use the Continuity Test to score positions of domain boundaries. Boundaries that divide the protein into domains contigous in sequence score more highly.<br />
; NMADOMAIN WEIGHT EQUALITY <WEIGHT><br />
: Weight factor for the the Equality Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT SPHERICITY <WEIGHT><br />
: Weight factor for the the Density Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT DENSITY <WEIGHT><br />
: Weight factor for the the Equality Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT CONTINUITY <WEIGHT><br />
: Weight factor for the the Continuity Test in the total Domain Score.<br />
* Default: NMADOMAIN ENABLE OFF<br />
* Default: NMADOMAIN NUMBER 2<br />
* Default: NMADOMAIN EQUALITY ON<br />
* Default: NMADOMAIN SPHERICITY ON <br />
* Default: NMADOMAIN DENSITY ON<br />
* Default: NMADOMAIN CONTINUITY OFF<br />
* Default: NMADOMAIN WEIGHT EQUALITY 1<br />
* Default: NMADOMAIN WEIGHT SPHERICITY 4 <br />
* Default: NMADOMAIN WEIGHT DENSITY 1<br />
* Default: NMADOMAIN WEIGHT CONTINUITY 1<br />
* Default: NMADOMAIN DDM SLIDER 0<br />
* Default: NMADOMAIN DDM STEP 50<br />
* Default: NMADOMAIN DDM MIN 1<br />
* Default: NMADOMAIN DDM MAX 5<br />
* Default: NMADOMAIN JOIN MIN -1<br />
* Default: NMADOMAIN JOIN MAX -1<br />
* Default: NMADOMAIN SEQUENCE MIN 0<br />
* Default: NMADOMAIN SEQUENCE MAX 1<br />
* Default: NMADOMAIN DISTANCE MIN 7<br />
* Default: NMADOMAIN DISTANCE MAX 14<br />
setNMAD_ENAB(bool)<br />
addNMAD_NUMB(int <NUMB>) <br />
setNMAD_EQUA(bool)<br />
setNMAD_SPHE(bool)<br />
setNMAD_DENS(bool)<br />
setNMAD_CONT(bool)<br />
setNMAD_WEIG_EQUA(float <WEIGHT>) <br />
setNMAD_WEIG_SPHE(float <WEIGHT>) <br />
setNMAD_WEIG_DENS(float <WEIGHT>)<br />
setNMAD_WEIG_CONT(float <WEIGHT>)<br />
setNMAD_DDM_SLID(int <VAL>) <br />
setNMAD_DDM_STEP(int <VAL>) <br />
setNMAD_DDM_MINI(int <VAL>) <br />
setNMAD_DDM_MAXI(int <VAL>) <br />
setNMAD_JOIN_MINI(int <VAL>) <br />
setNMAD_JOIN_MAXI(int <VAL>) <br />
setNMAD_SEQU_MINI(int <VAL>) <br />
setNMAD_SEQU_MAXI(int <VAL>) <br />
setNMAD_DIST_MINI(float <VAL>) <br />
setNMAD_DIST_MAXI(float <VAL>)<br />
<br />
==[[Image:User2.gif|link=]]NMAPDB== <br />
; NMAPDB PERTURB [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; NMAPDB MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. <br />
; NMAPDB COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
; NMAPDB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; NMAPDB RMS CLASH <CLASH> <br />
; NMAPDB RMS STRETCH <STRETCH> <br />
; NMAPDB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until either the C-alpha atoms clash with (come within CLASH Ångstroms of) other C-alpha atoms, the distances between C-alpha atoms STRETCH too far (note that normal modes do not preserve the geometry) or the MAXRMS deviation has been reached.<br />
; NMAPDB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; NMAPDB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: NMAPDB MODE 7 <br />
* Default: NMAPDB COMBINATION 3<br />
* Default: NMAPDB PERTURB RMS <br />
* Default: NMAPDB RMS STEP 0.3 <br />
* Default: NMAPDB RMS STRETCH 5.0 <br />
* Default: NMAPDB RMS CLASH 2.0<br />
* Default: NMAPDB RMS MAXRMS 0.5<br />
* Default: NMAPDB RMS DIRECTION TOFRO<br />
setNMAP_PERT(str [ "RMS" | "DQ" ])<br />
addNMAP_MODE(int <MODE>) <br />
setNMAP_COMB(int <NMAX>)<br />
setNMAP_RMS_CLAS(float <CLASH>) <br />
setNMAP_RMS_STRE(float <STRETCH>) <br />
setNMAP_RMS_MAXI(float <MAX>)<br />
setNMAP_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addNMAP_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>BEST | <sup>2</sup>ALLOW | <sup>3</sup>PERCENT | <sup>4</sup>ALL ]<br />
: <sup>1</sup>Allow the best packing solutions only, provided the total number of clashes does not exceed ALLOWED_CLASHES<br />
: <sup>2</sup>Allow all solutions that pack with number of C-alpha clashes less than ALLOWED_CLASHES<br />
: <sup>3</sup>Allow up to the ALLOWED_CLASHES percentage of C-alpha atoms of the model structure to clash<br />
: <sup>4</sup>Allow all solutions (no packing test)<br />
: If the model is RNA or DNA, phosphate (P) and carbon atoms (C3* and C4*) in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes. The atom names must start in column 14 (leaving one space at the beginning of the field), and the residue names must be right-justified (i.e. in column 20 for the single-letter names of ribonucleotides such as A, or in columns 19-20 for the two letter names of deoxyribonucleotides such as DA).<br />
; PACK CUTOFF <ALLOWED_CLASHES> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (ZSCORE keyword).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
;[[Image:Expert.gif|24px]] PACK DISTANCE <DISTANCE><br />
: Distance within which C-alpha atoms clash given by DISTANCE Ångstroms. If the model is RNA or DNA, phosphate and carbon atoms in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes<br />
;[[Image:Expert.gif|24px]] PACK TRACE [ON|OFF]<br />
: Toggle whether or not to only use Trace atoms (C-alpha atoms in proteins and P in RNA/DNA) for packing analysis, or all atoms. Only recommended to be OFF for use with small fragments.<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK QUICK ON<br />
* Default: PACK COMPACT ON<br />
* Default: PACK DISTANCE 3.0<br />
setPACK_SELE(str ["BEST"|"ALLOW"|"PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_COMP(bool)<br />
setPACK_DIST(float <DISTANCE>)<br />
setPACK_TRAC(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for the rotation function (ROT) or translation function (TRA) satisfying selection criteria are saved<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH MEHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<br />
; PURGE TRA ENABLE [ON|OFF]<br />
: Toggle for whether to purge the solution list from the RF or TF and after the refinement steps (in AUTO mode) according to the best solution found so far.<br />
; PURGE ROT PERCENT <PERC><br />
; PURGE TRA PERCENT <PERC><br />
: PERC is the percent of the difference between the top solution and the mean at which to purge the solutions.<br />
; PURGE ROT NUMBER <NUM><br />
; PURGE TRA NUMBER <NUM><br />
: NUM is the number of solutions to retain in purging. The number taken is the minimum of the number found with the PERCENT cutoff and the NUMBER cutoff. If NUM is zero then the number is not used as a selection criteria.<br />
* Default: PURGE ROT ENABLE ON PERC 75 NUM 0<br />
* Default: PURGE TRA ENABLE ON PERC 75 NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
; RESOLUTION AUTO LOW <LORES> <br />
: Low resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO_AUTO_LOW(float <LORES>)<br />
setRESO(float <HIRES>,float <LORES>) <br />
setRESO_AUTO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
* Default: ROTATE VOLUME FULL<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS REFINE ROTATION [ON | OFF]<br />
: Use TNCS correction method that includes a rotation refinement of the two TNCS related rotations (to separate the rotation function results) before the translation function<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes (GRID OFF). Central value for grid search (GRID ON).<br />
; TNCS ROTATION GRID [ON | OFF]<br />
: Refine the initial rotation angle starting from a grid of orientations around the starting angle (default 0,0,0). Grid controlled by RANGE and SAMPLING. The best refined rotational angle will be selected.<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minium distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS USE ON<br />
* Default: TNCS REFINE ROTATION OFF<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION GRID ON<br />
* Default: TNCS ROTATION SAMPLING 0<br />
* Default: TNCS ROTATION RANGE 0<br />
* Default: TNCS VARIANCE RMS 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15<br />
* Default: TNCS NMOL 2<br />
setTNCS_USE(bool)<br />
setTNCS_REFI_ROTA(bool)<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>)<br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>) <br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_NMOL(int <NMOL>)<br />
<br />
==[[Image:User2.gif|link=]]TRANSLATE== <br />
; TRANSLATE VOLUME [ <sup>1</sup>FULL| <sup>2</sup>REGION| <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search along line. <br />
: <sup>3</sup> Search region.<br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATE START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATE END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATE POINT <X Y Z><br />
; <sup>4</sup>TRANSLATE RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATE [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
* Default: TRANSLATE VOLUME FULL<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with SEARCH METHOD FAST. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
==[[Image:Expert.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''SOLP [ON|OFF] LAST [ON|OFF} NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACMR PROTOCOL DEFAULT<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <SOLP>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD K [ON|OFF] B [ON|OFF] SIGMA [ON|OFF] XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(bool <K>,bool <nowiki><B></nowiki>,bool <SIGMA>,<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]NMAMETHOD== <br />
; NMAMETHOD OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>CA | <sup>3</sup>ALL ] <br />
: Define the atoms used for the normal mode analysis. <br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use C-alpha atoms only to determine the modes.<br />
: <sup>3</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; NMAMETHOD MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; NMAMETHOD NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; NMAMETHOD RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; NMAMETHOD FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: NMAMETHOD OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setNMAM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setNMAM_RTB_MAXB(float <MAXB>)<br />
setNMAM_RTB_NRES(float <NRES>) <br />
setNMAM_RADI(float <RADIUS>) <br />
setNMAM_FORC(float <FORCE>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with search method [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (MODE = MR_BRF or MR_FRF)<br />
* Default: SAMP = dmin/5; (MODE = MR_BTF)<br />
* Default: SAMP = dmin/4; (MODE = MR_FTF)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS MIN <L> <br />
: The binning of the data. L = minimum number of bins.<br />
; BINS MAX <H> <br />
: The binning of the data. H = maximum number of bins.<br />
; BINS WIDTH <W><br />
: The binning of the data. W = width of the bins in number of reflections<br />
; BINS CUBIC <A> <nowiki><B></nowiki> <C><br />
: The binning of the data. A B C are the coefficients for the binning function A(S*S*S)+B(S*S)+CS where S = (1/resolution). Cubic coefficients restricted to monotonically increasing function: A >0, B >0, C >0 and either (a) A=B=0 or (b) A=0 or (c) B=0<br />
* Default: BINS MIN 6 MAX 50 WIDTH 500 CUBIC 0 1 0 <br />
setBINS_MINI(float <L>)<br />
setBINS_MAXI(float <H>)<br />
setBINS_WIDT(float <W>)<br />
setBINS_CUBI(dvect3 <A B C>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for molecular Bfactor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 10<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; CELL <A> <nowiki><B></nowiki> <C> <ALPHA> <BETA> <GAMMA><br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]CLMN== <br />
; CLMN SPHERE <SPHERE><br />
: Radius for the decomposition of the Patterson in Ångstroms. If it is 0, the radius defaults to twice the mean radius of the ENSEMBLE.<br />
; CLMN LMIN <LMIN><br />
: Lower limit of L values.<br />
; CLMN LMAX <LMAX><br />
: Upper limit of L values. The largest L value used in the calculation is the minimum of LMAX and 2&pi; * SPHERE/dmin.<br />
* Default: CLMN LMIN 4<br />
* Default: CLMN LMAX 100<br />
* Default: CLMN SPHE 0<br />
setCLMN_SPHE(float <SPHERE>) <br />
setCLMN_LMIN(float <LMIN>) <br />
setCLMN_LMAX(float <LMAX>)<br />
<br />
==[[Image:Developer.gif|link=]]FFTS==<br />
; FFTS MIN <ATOMS_MIN> MAX <ATOMS_MAX><br />
: The minimum and maximum number of atoms of the range between which direct summation and fft methods are tested to see which is faster for structure factor and gradient calcuation (for this unit cell and resolution). For a number of atoms below ATOMS_MIN direct structure factor calculation is always used, and for a number of atoms above ATOMS_MAX ffts are always used for the structure factor calculation and the gradient calculations. Direct summation is always used for the curvatures. Use FFTS MIN 0 MAX O to always use ffts.<br />
* Default: FFTS MIN 20 MAX 80<br />
setFFTS_MINI(float <ATOMS_MIN>) <br />
setFFTS_MAXI(float <ATOMS_MAX>)<br />
<br />
==[[Image:Developer.gif|link=]]INTEGRATION==<br />
; INTEGRATION FIXED [ON|OFF]<br />
: Fix the number of integration points or determine the number of angular steps in the integration by the variance of the function<br />
; INTEGRATION STEP <STEP><br />
: Number of steps in angular integration of function if FIXED number of points<br />
* Default: INTEGRATION FIXED OFF<br />
setINTE_FIXE(bool <True|False>) <br />
setINTE_STEP(float <STEP>)<br />
<br />
==[[Image:Developer.gif|link=]]MACHL== <br />
; MACHL PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of Hendrickson-Lattman coefficients<br />
; MACHL COEF [ON|OFF] ''NCYCle <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of Hendrickson-Lattman coefficients. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACHL PROTOCOL DEFAULT<br />
setMACH_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACH(bool <COEF>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
;NORMALIZATION BINS <B1 B2 ...> ANISO <HH> <KK> <LL> <HK> <HL> <KL> SOLK <SOLK> SOLB <SOLB><br />
: The normalization factors that correct for anisotropy in the data<br />
setNORM_BINS(float_array <B1 B2 ...>)<br />
setNORM_ANIS(dmat6 <HH KK LL HK HL KL>)<br />
setNORM_SOLK(float <SOLK>) <br />
setNORM_SOLB(float <SOLB>) <br />
setNORM(float_array <B1 B2 ...> ,dmat6 <HH KK LL HK HL KL>,float <SOLK>,float <SOLB>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS FSOL <FSOL> BSOL <BSOL> FIXB [ON|OFF]<br />
: Babinet solvent parameters for Sigma(A) curves. If FIXB is OFF, then BSOL is calculated from FSOL using the formula BSOL = 99.1 + 5.79*exp(4.03*FSOL) from Glykos & Kokkinkdis Acta Cryst D56 p1070 (2000), otherwise BSOL is fixed at the input (or default) value.<br />
; SOLPARAMETERS RESTRAIN [ON|OFF]<br />
: Restrain the Babinet solvent parameters to the initial values during refinement.<br />
; SOLPARAMETERS RESOLUTION <HIRES><br />
; Do not apply Babinet solvent correction terms to resolutions higher than HIRES.<br />
* Default: SOLPARAMETERS FSOL 0.69 BSOL 378 FIXB ON<br />
* Default: SOLPARAMETERS RESTRAINT OFF<br />
* Default: SOLPARAMETERS RESOLUTION 0<br />
setSOLP_FSOL(float <FSOL>) <br />
setSOLP_BSOL(float <BSOL>)<br />
setSOLP_FIXB(bool) <br />
setSOLP_REST(bool)<br />
<br />
==[[Image:Developer.gif|link=]]SORT==<br />
; SORT [ON|OFF]<br />
: Sort the reflections into resolution order upon reading MTZ file, for performance gain in molecular replacement<br />
* Default: SORT ON<br />
setSORT(bool)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET==<br />
; TARGET FRF [LERF1|LERF2|CROWTHER]<br />
: Target function for fast rotation searches (2)<br />
; TARGET FTF [LETF1|LETF2|CORRELATION]<br />
: Target function for fast translation searches (3)<br />
* Default: TARGET FRF LERF1 <br />
* Default: TARGET FTF LETF1<br />
setTARG_FRF(str ["LERF1"|"LERF2"|"CROWTHER"])<br />
setTARG_FTF(str ["LETF1"|"LETF2"|"CORRELATION"])<br />
<br />
==[[Image:Developer.gif|link=]]VARSAD==<br />
; VARSAD [ K <N> | B <N> | SIGMA <N> | SA <B1 B2 …> | SB <B1 B2 …> | SP <B1 B2 …> | SD <B1 B2 …> | PK <N> | PB <N>]<br />
: SAD variance parameters SA and SB (the real and imaginary components of Sigma Minus), SP (Sigma Plus) and SD (Sigma Delta) by resolution bin, the overall scale (K) and B-factor (B) for the anomalous scatterer model, the overall scale (PK) and B-factor (PB) for the partial structure (if given), and sigma-scale (SIGMA).<br />
setVARS(float_array <VARIANCES></div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Keywords&diff=1514Keywords2012-06-27T16:31:29Z<p>WikiSysop: /* link=NMAPDB */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
'''These keywords are for the current (nightly build) release of Phaser through [http://www.phenix-online.org/download/ Phenix] .'''<br />
<br />
===Phaser Executable===<br />
<br />
The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].<br />
<br />
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. <br />
<br />
*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]<br />
<br />
*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]<br />
<br />
*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]<br />
<br />
*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]<br />
<br />
*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]<br />
<br />
<br />
===Python Interface===<br />
<br />
Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. <br />
<br />
The python interface uses standard python and cctbx/scitbx variable types.<br />
<br />
str string<br />
float double precision floating point<br />
Miller cctbx::miller::index<int> <br />
dvect3 scitbx::vec3<float> <br />
dmat33 scitbx::mat3<float> <br />
'''type'''_array scitbx::af::shared<'''type'''> arrays<br />
<br />
=Basic Keywords=<br />
==[[Image:User1.gif|link=]]ATOM== <br />
; ATOM CRYSTAL <XTALID> PDB <FILENAME><br />
: Definition of atom positions using a pdb file.<br />
; ATOM CRYSTAL <XTALID> HA <FILENAME><br />
: Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.).<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> <br />
: Minimal definition of atom position. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged. Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.<br />
; ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME><br />
: Full definition of atom position including B-factor.<br />
;ATOM CHANGE BFACTOR WILSON [ON|OFF]<br />
: Reset all atomic B-factors to the Wilson B-factor.<br />
; ATOM CHANGE SCATTERER <SCATTERER><br />
:Reset all atomic scatterers to element (or cluster) type.<br />
setATOM_PDB(str <XTALID>,str <FILENAME>)<br />
setATOM_HA(str <XTALID>,str <FILENAME>)<br />
addATOM(str <XTALID>,str <TYPE>,<br />
float <X>,float <Y>,float <Z>,float <OCC>)<br />
addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,<br />
dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,<br />
bool <ANOU>,dmat6 <HH KK LL HK HL KL>,<br />
bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,<br />
str <SITE_NAME>)<br />
setATOM_CHAN_BFAC_WILS(bool)<br />
setATOM_CHAN_SCAT(str <TYPE>)<br />
<br />
==[[Image:User1.gif|link=]]CLUSTER== <br />
; CLUSTER PDB <PDBFILE><br />
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX. Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.<br />
setCLUS_PDB(str <PDBFILE>)<br />
<br />
==[[Image:User1.gif|link=]]COMPOSITION== <br />
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]<br />
: Alternative ways of defining composition<br />
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)<br />
: <sup>2</sup> Composition entered by solvent content.<br />
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight<br />
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT><br />
: Specified SOLVENT content<br />
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM><br />
: Contribution to composition of the ASU. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.<br />
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM><br />
: Add NUM copies of an atom (usually a heavy atom) to the composition<br />
* Default: COMPOSITION BY ASU<br />
setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])<br />
setCOMP_PERC(float <SOLVENT>)<br />
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)<br />
addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)<br />
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)<br />
addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)<br />
addCOMP_ATOM(str <TYPE>,float <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]CRYSTAL== <br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG-><br />
: Columns of MTZ file to read for this (anomalous) dataset<br />
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF><br />
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.<br />
setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->) <br />
setCRYS_MEAN_LABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]ENSEMBLE== <br />
; ENSEMBLE <MODLID> PDB <PDBFILE> [RMS <RMS><sup>1</sup>|IDENTITY <ID><sup>2</sup>|CARD ON<sup>3</sup>] ''{PDB <PDBFILE> [RMS <RMS>|IDENTITY <ID>|CARD ON] }…''<br />
: The names of the PDB files used to build the ENSEMBLE, and either<br />
: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure<br />
: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.<br />
: <sup>3</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard because the atom list for the different models need not be the same.<br />
; ENSEMBLE <MODLID> HKLIN <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX> <EY> <EZ> RMS <RMS> CENTRE <CX> <CY> <CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW><br />
: An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms.<br />
; ENSEMBLE <MODLID> FRACTION <FRAC_SCAT><br />
: Fraction scattering of ensemble entered directly rather than calculated from composition<br />
;[[Image:Expert.gif|24px]] ENSEMBLE <MODLID> BINS MIN <L> MAX <H> WIDTH <W> CUBIC <A> <nowiki><B></nowiki> <C><br />
: Bins for the calculated data for MODLID (in P1 cell). See [[#BINS | BINS]] for details of sub-keywords.<br />
;[[Image:Expert.gif|24px]] ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]<br />
: Toggle to disable checking of deviation between models in an ensemble. '''Use with extreme caution'''. Results of computations are not guaranteed to be sensible.<br />
* Default: ENSEMBLE <MODLID> BINS MIN 5 MAX 200 WIDTH 1000 CUBIC 0 1 0<br />
* Default: ENSEMBLE <MODLID> DISABLE CHECK OFF<br />
addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) <br />
addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>)<br />
addENSE_CARD(str <MODLID>,str <FILE>,bool)<br />
setENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,<br />
float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>)<br />
setENSE_BINS_MIN(str <MODLID>,float <L>)<br />
setENSE_BINS_MAX(str <MODLID>,float <H>)<br />
setENSE_BINS_WIDTH(str <MODLID>,float <W>)<br />
setENSE_BINS_CUBIC(str <MODLID>,dvect3 <A> <nowiki><B></nowiki> <C>)<br />
setENSE_FRAC(str <MODLID>,float <FRAC_SCAT>)<br />
<br />
==[[Image:User1.gif|link=]]HKLIN==<br />
; HKLIN <FILENAME><br />
: The mtz file containing the data<br />
setHKLI(str <FILENAME>)<br />
<br />
==[[Image:User1.gif|link=]]JOBS== <br />
; JOBS <NUM><br />
: Number of processors to use in parallelized sections of code<br />
* Default: JOBS 2<br />
setJOBS(int <NUM>)<br />
<br />
==[[Image:User1.gif|link=]]LABIN== <br />
; LABIN F = <F> SIGF = <SIGF><br />
: Columns in mtz file. F must be given. SIGF should be given but is optional<br />
setLABI(str <F>,str <SIGF>)<br />
<br />
==[[Image:User1.gif|link=]]MODE==<br />
; MODE [ ANO | CCA | NMA | NCS | MR_AUTO | MR_FRF | MR_FTF | MR_BRF | MR_BTF | MR_RNP | MR_LLG | MR_PAK | EP_AUTO | EP_SAD]<br />
: The mode of operation of Phaser. The different modes are described in a separate page on [[Keyword Modes]]<br />
ResultANO r = runANO(InputANO)<br />
ResultCCA r = runCCA(InputCCA)<br />
ResultNMA r = runNMA(InputNMA)<br />
ResultMR r = runMR_AUTO(InputMR_AUTO)<br />
ResulrMR_RF r = runMR_FRF(InputMR_FRF)<br />
ResultMR_TF r = runMR_FTF(InputMR_FTF)<br />
ResultMR_RF r = runMR_BRF(InputMR_BRF)<br />
ResultMR_TF r = runMR_BTF(InputMR_BTF)<br />
ResultMR r = runMR_RNP(InputMR_RNP)<br />
ResultMR r = runMR_LLG(InputMR_LLG)<br />
ResultMR r = runMR_PAK(InputMR_PAK)<br />
ResultEP r = runEP_AUTO(InputEP_AUTO)<br />
ResultP_SAD r = runEP_SAD(InputEP_SAD)<br />
<br />
==[[Image:User1.gif|link=]]PARTIAL== <br />
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID><br />
: The partial structure for SAD refinement.<br />
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID><br />
: The partial electron density for SAD refinement.<br />
setPART_PDB(str <PDBFILE>)<br />
setPART_HKLI(str <MTZFILE>) <br />
setPART_VARI(str ["ID"|"RMS"])<br />
setPART_DEVI(float <RMS_ID>)<br />
<br />
==[[Image:User1.gif|link=]]SEARCH==<br />
; SEARCH ENSEMBLE <MODLID> ''{OR ENSEMBLE <MODLID>}… NUMBER <NUM>''<br />
: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).<br />
; SEARCH ORDER AUTO [ON|OFF]<br />
: Search in the "best" order as estimated using estimated rms deviation and completeness of models.<br />
; SEARCH METHOD [FULL|FAST]<br />
: Search using the "full search" or "fast search" algorithms.<br />
; SEARCH DEEP [ON|OFF]<br />
: Search method FAST only. Flag to control whether or not the cuttoff for the peaks in the rotation function is reduced if there is no TFZ over ZSCORE_CUTOFF in the first search.<br />
; SEARCH DOWN PERCENT <PERC><br />
: Search method FAST only. Percentage to reduce rotation function cutoff if there is no TFZ over ZSCORE_CUTOFF in first search.<br />
; SEARCH BFACTOR <BFAC><br />
: B-factor applied to search molecule (or atom).<br />
* Default: SEARCH METHOD FAST<br />
* Default: SEARCH ORDER AUTO ON<br />
* Default: SEARCH DEEP ON<br />
* Default: SEARCH DOWN PERCENT 25<br />
* Default: SEARCH BFACTOR 0<br />
addSEAR_ENSE_NUMB(str <MODLID>,int <NUM>) <br />
addSEAR_ENSE_OR_ENSE_NUMB(string_array <MODLIDS>,int <NUM>) <br />
setSEAR_ORDE_AUTO(bool])<br />
setSEAR_METH(str [ "FULL" | "FAST" ])<br />
setSEAR_DOWN_PERC(float <PERC>)<br />
setSEAR_BFAC(float <BFAC>)<br />
<br />
==[[Image:User1.gif|link=]]SGALTERNATIVE==<br />
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]<br />
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]<br />
: <sup>1</sup> Test all possible space groups, <br />
: <sup>2</sup> Test the given space group and its enantiomorph.<br />
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.<br />
: <sup>4</sup> Do not test alternative space groups.<br />
; SGALTERNATIVE TEST <SG><br />
: Alternative space groups to test. Multiple test space groups can be entered.<br />
; SGALTERNATIVE SORT [ON|OFF]<br />
: Sort alternative space group list in order of frequency of occurrence.<br />
* Default: SGALTERNATIVE SELECT HAND<br />
* Default: SGALTERNATIVE SORT ON<br />
setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) <br />
addSGAL_TEST(str <SG>)<br />
setSGAL_SORT(bool)<br />
<br />
==[[Image:User1.gif|link=]]SOLUTION==<br />
; SOLUTION SET <ANNOTATION><br />
: Start new set of solutions <br />
; SOLUTION TEMPLATE <ANNOTATION><br />
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.<br />
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''<br />
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation. BFAC default to 0, MULT (for multiplicity) defaults to 1.<br />
; SOLUTION SPACEGROUP <SG><br />
: Space Group of the solution (if alternative spacegroups searched).<br />
; SOLUTION ENSEMBLE <MODLID> VRMS <V1> <V2> ...<br />
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).<br />
; SOLUTION SOLPAR FSOL <FSOL><br />
; SOLUTION SOLPAR BSOL <BSOL><br />
; SOLUTION SOLPAR FIXB <FIXB><br />
: Solvent parameters for the solution (if refined). See [[#SOLPARAMETERS | SOLPARAMETERS]] keyword for details.<br />
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RFZ <RFZ><br />
: Rotation List for translation function<br />
; SOLUTION ORIGIN ENSEMBLE <MODLID><br />
: Create solution for ensemble MODLID at the origin<br />
addSOLU_SET(str <ANNOTATION>) <br />
addSOLU_TEMPLATE(str <ANNOTATION>) <br />
addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,<br />
float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>) <br />
setSOLU_SPAC(str <SG>)<br />
addSOLU_ENSE_VRMS(str <MODLID>, float_array <VARIANCES>) <br />
setSOLU_SOLP_FSOL(float)<br />
setSOLU_SOLP_BSOL(float)<br />
setSOLU_SOLP_FIXB(bool)<br />
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)<br />
addSOLU_ORIG_ENSE(string <MODLID>)<br />
<br />
==[[Image:User1.gif|link=]]SPACEGROUP==<br />
; SPACEGROUP <SG><br />
: Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group can be entered in one of three ways<br />
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)<br />
#The international tables number, which gives standard setting e.g. 19 <br />
#The Hall symbols e.g. P 2ac 2ab<br />
* Default: Read from MTZ file<br />
setSPAC_NUM(int <NUM>)<br />
setSPAC_NAME(string <HM>)<br />
setSPAC_HALL(string <HALL>)<br />
<br />
==[[Image:User1.gif|link=]]WAVELENGTH== <br />
; WAVELENGTH <LAMBDA> <br />
: The wavelengh at which the SAD dataset was collected<br />
setWAVE(float <LAMBDA>)<br />
<br><br />
<br><br />
<br />
=Output Control Keywords=<br />
==[[Image:Output.png|link=]]DEBUG== <br />
; DEBUG [ON|OFF]<br />
: Extra verbose output for debugging<br />
* Default: DEBUG OFF<br />
setDEBU(bool) <br />
<br />
==[[Image:Output.png|link=]]EIGEN==<br />
; EIGEN WRITE [ON|OFF]<br />
; EIGEN READ <EIGENFILE><br />
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the atomic Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical (or default) input for keyword NMAMethod. Use WRITe to control whether or not the eigenfile is written when not using the READ mode.<br />
* Default: EIGEN WRITE ON<br />
setEIGE_WRIT(bool)<br />
setEIGE_READ(str <EIGENFILE>)<br />
<br />
==[[Image:Output.png|link=]]HKLOUT== <br />
; HKLOUT [ON|OFF]<br />
: Flags for output of an mtz file containing the phasing information<br />
* Default: HKLOUT ON<br />
setHKLO(bool) <br />
<br />
==[[Image:Output.png|link=]]KEYWORDS== <br />
; KEYWORDS [ON|OFF]<br />
: Write output Phaser .sol file (.rlist file for rotation function)<br />
* Default: KEYWORDS ON<br />
setKEYW(bool) <br />
<br />
==[[Image:Output.png|link=]]MUTE== <br />
; MUTE [ON|OFF]<br />
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.<br />
* Default: MUTE OFF<br />
setMUTE(bool) <br />
<br />
==[[Image:Output.png|link=]]TITLE==<br />
; TITLE <TITLE><br />
: Title for job<br />
* Default: TITLE [no title given]<br />
setTITL(str <TITLE>)<br />
<br />
==[[Image:Output.png|link=]]TOPFILES== <br />
; TOPFILES <NUM><br />
: Number of top pdbfiles or mtzfiles to write to output.<br />
* Default: TOPFILES 1<br />
setTOPF(int <NUM>) <br />
<br />
==[[Image:Output.png|link=]]ROOT== <br />
; ROOT <FILEROOT><br />
: Root filename for output files (e.g. FILEROOT.log)<br />
* Default: ROOT PHASER<br />
setROOT(string <FILEROOT>)<br />
<br />
==[[Image:Output.png|link=]]VERBOSE== <br />
; VERBOSE [ON|OFF] <br />
: Toggle to send verbose output to log file.<br />
* Default: VERBOSE OFF<br />
setVERB(bool) <br />
<br />
==[[Image:Output.png|link=]]XYZOUT== <br />
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]''<br />
: Toggle for output coordinate files. If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). <br />
* Default: XYZOUT OFF (Rotation functions)<br />
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)<br />
setXYZO(bool) <br />
setXYZO_ENSE(bool)<br />
<br><br />
<br><br />
<br />
=Advanced Keywords=<br />
==[[Image:User2.gif|link=]]ELLG==<br />
; ELLG USE [ON|OFF]<br />
: Use expected LLG to determine resolution limits and search order<br />
; ELLG TARGET <TARGET><br />
: Target value for expected LLG for determining resolution limits and search order<br />
* Default: ELLG USE ON<br />
* Default: ELLG TARGET 120<br />
setELLG_USE(bool <True|False>)<br />
setELLG_TARG(float <TARGET>)<br />
<br />
==[[Image:User2.gif|link=]]HAND==<br />
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]<br />
: Hand of heavy atoms for experimental phasing<br />
: <sup>1</sup>Phase using the given hand of heavy atoms <br />
: <sup>2</sup>Phase using other hand of heavy atoms <br />
: <sup>3</sup>Phase using both hands of heavy atoms<br />
* Default: HAND BOTH<br />
setHAND(str [ "OFF" | "ON" | "BOTH" ])<br />
<br />
==[[Image:User2.gif|link=]]LLGCOMPLETE==<br />
; LLGComplete COMPLETE [ON|OFF]<br />
: Toggle for structure completion by log-likelihood gradient maps<br />
; LLGComplete SCATTERER <TYPE> <br />
: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer<br />
; LLGComplete CLASH <CLASH> <br />
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (default determined by resolution, flagged by CLASH=0)<br />
; LLGComplete SIGMA <Z><br />
: Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps<br />
; LLGComplete NCYC <NMAX><br />
: Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.<br />
; LLGComplete MAPS [ON|OFF]<br />
: Output map coefficients to mtz file<br />
; LLGComplete METHOD [IMAGINARY|ATOMTYPE]<br />
: Pick peaks from the imaginary map only or from all the completion atomtype maps.<br />
* Default: LLGCOMPLETE COMPLETE OFF<br />
* Default: LLGCOMPLETE CLASH 0<br />
* Default: LLGCOMPLETE SIGMA 6<br />
* Default: LLGComplete NCYC 50<br />
* Default: LLGComplete MAPS OFF<br />
* Default: LLGComplete METHOD ATOMTYPE<br />
setLLGC_COMP(bool <True|False>) <br />
setLLGC_CLAS(float <CLASH>) <br />
setLLGC_SIGM(float <Z>) <br />
setLLGC_NCYC(int <NMAX>)<br />
setLLGC_MAPS(bool <True|False>)<br />
setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])<br />
<br />
==[[Image:User2.gif|link=]]NMADOMAIN== <br />
; NMADOMAIN ENABLE [ON| OFF] <br />
: Use NMA to determine domain structure of protein rather than using it to perturb a pdb file<br />
; NMADOMAIN NUMBER <NUMB><br />
:Number of domains into which to split the protein<br />
; NMADOMAIN EQUALITY [ON| OFF] <br />
: Use the Equality Test to score positions of domain boundaries. Boundaries that divide the protein more equally score more highly.<br />
; NMADOMAIN SPHERICITY [ON| OFF] <br />
: Use the Sphericity Test to score positions of domain boundaries. Boundaries that divide the protein into more spherical domains score more highly.<br />
; NMADOMAIN DENSITY [ON| OFF] <br />
: Use the Density Test to score positions of domain boundaries. Boundaries that divide the protein into domains more densely packed with atoms score more highly.<br />
; NMADOMAIN CONTINUITY [ON| OFF] <br />
: Use the Continuity Test to score positions of domain boundaries. Boundaries that divide the protein into domains contigous in sequence score more highly.<br />
; NMADOMAIN WEIGHT EQUALITY <WEIGHT><br />
: Weight factor for the the Equality Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT SPHERICITY <WEIGHT><br />
: Weight factor for the the Density Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT DENSITY <WEIGHT><br />
: Weight factor for the the Equality Test in the total Domain Score.<br />
; NMADOMAIN WEIGHT CONTINUITY <WEIGHT><br />
: Weight factor for the the Continuity Test in the total Domain Score.<br />
* Default: NMADOMAIN ENABLE OFF<br />
* Default: NMADOMAIN NUMBER 2<br />
* Default: NMADOMAIN EQUALITY ON<br />
* Default: NMADOMAIN SPHERICITY ON <br />
* Default: NMADOMAIN DENSITY ON<br />
* Default: NMADOMAIN CONTINUITY OFF<br />
* Default: NMADOMAIN WEIGHT EQUALITY 1<br />
* Default: NMADOMAIN WEIGHT SPHERICITY 4 <br />
* Default: NMADOMAIN WEIGHT DENSITY 1<br />
* Default: NMADOMAIN WEIGHT CONTINUITY 1<br />
* Default: NMADOMAIN RMS CLASH 2.0<br />
* Default: NMADOMAIN RMS MAXRMS 0.5<br />
* Default: NMADOMAIN RMS DIRECTION TOFRO<br />
setNMAD_ENAB(bool)<br />
addNMAD_NUMB(int <NUMB>) <br />
setNMAD_EQUA(bool)<br />
setNMAD_SPHE(bool)<br />
setNMAD_DENS(bool)<br />
setNMAD_CONT(bool)<br />
setNMAD_WEIG_EQUA(float <WEIGHT>) <br />
setNMAD_WEIG_SPHE(float <WEIGHT>) <br />
setNMAD_WEIG_DENS(float <WEIGHT>)<br />
setNMAD_WEIG_CONT(float <WEIGHT>)<br />
<br />
==[[Image:User2.gif|link=]]NMAPDB== <br />
; NMAPDB PERTURB [RMS| DQ] <br />
: Perturb the structure by rms devitations along the modes, or by set dq increments<br />
; NMAPDB MODE <M1> ''{MODE <M2>…}'' <br />
: The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially. <br />
; NMAPDB COMBINATION <NMAX><br />
: Controls how many modes are present in any combination.<br />
; NMAPDB RMS STEP <RMS><br />
: Increment in rms Ångstroms between pdb files to be written. <br />
; NMAPDB RMS CLASH <CLASH> <br />
; NMAPDB RMS STRETCH <STRETCH> <br />
; NMAPDB RMS MAX <MAXRMS><br />
: The structure will be perturbed along each mode until either the C-alpha atoms clash with (come within CLASH Ångstroms of) other C-alpha atoms, the distances between C-alpha atoms STRETCH too far (note that normal modes do not preserve the geometry) or the MAXRMS deviation has been reached.<br />
; NMAPDB RMS DIRECTION [FORWARD|BACKWARD|TOFRO] <br />
: The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.<br />
; NMAPDB DQ <DQ1> ''{DQ <DQ2>…}''<br />
: Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.<br />
* Default: NMAPDB MODE 7 <br />
* Default: NMAPDB COMBINATION 3<br />
* Default: NMAPDB PERTURB RMS <br />
* Default: NMAPDB RMS STEP 0.3 <br />
* Default: NMAPDB RMS STRETCH 5.0 <br />
* Default: NMAPDB RMS CLASH 2.0<br />
* Default: NMAPDB RMS MAXRMS 0.5<br />
* Default: NMAPDB RMS DIRECTION TOFRO<br />
setNMAP_PERT(str [ "RMS" | "DQ" ])<br />
addNMAP_MODE(int <MODE>) <br />
setNMAP_COMB(int <NMAX>)<br />
setNMAP_RMS_CLAS(float <CLASH>) <br />
setNMAP_RMS_STRE(float <STRETCH>) <br />
setNMAP_RMS_MAXI(float <MAX>)<br />
setNMAP_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) <br />
addNMAP_DQ(float <DQ>)<br />
<br />
==[[Image:User2.gif|link=]]PACK==<br />
; PACK SELECT [ <sup>1</sup>BEST | <sup>2</sup>ALLOW | <sup>3</sup>PERCENT | <sup>4</sup>ALL ]<br />
: <sup>1</sup>Allow the best packing solutions only, provided the total number of clashes does not exceed ALLOWED_CLASHES<br />
: <sup>2</sup>Allow all solutions that pack with number of C-alpha clashes less than ALLOWED_CLASHES<br />
: <sup>3</sup>Allow up to the ALLOWED_CLASHES percentage of C-alpha atoms of the model structure to clash<br />
: <sup>4</sup>Allow all solutions (no packing test)<br />
: If the model is RNA or DNA, phosphate (P) and carbon atoms (C3* and C4*) in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes. The atom names must start in column 14 (leaving one space at the beginning of the field), and the residue names must be right-justified (i.e. in column 20 for the single-letter names of ribonucleotides such as A, or in columns 19-20 for the two letter names of deoxyribonucleotides such as DA).<br />
; PACK CUTOFF <ALLOWED_CLASHES> <br />
: Limit on total number (or percent) of clashes <br />
; PACK QUICK [ON|OFF]<br />
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (ZSCORE keyword).<br />
; PACK COMPACT [ON|OFF]<br />
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).<br />
;[[Image:Expert.gif|24px]] PACK DISTANCE <DISTANCE><br />
: Distance within which C-alpha atoms clash given by DISTANCE Ångstroms. If the model is RNA or DNA, phosphate and carbon atoms in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes<br />
;[[Image:Expert.gif|24px]] PACK TRACE [ON|OFF]<br />
: Toggle whether or not to only use Trace atoms (C-alpha atoms in proteins and P in RNA/DNA) for packing analysis, or all atoms. Only recommended to be OFF for use with small fragments.<br />
* Default: PACK SELECT PERCENT<br />
* Default: PACK CUTOFF 5<br />
* Default: PACK QUICK ON<br />
* Default: PACK COMPACT ON<br />
* Default: PACK DISTANCE 3.0<br />
setPACK_SELE(str ["BEST"|"ALLOW"|"PERCENT"|"ALL"]) <br />
setPACK_CUTO(float <ALLOWED_CLASHES>)<br />
setPACK_QUIC(bool)<br />
setPACK_COMP(bool)<br />
setPACK_DIST(float <DISTANCE>)<br />
setPACK_TRAC(bool)<br />
<br />
==[[Image:User2.gif|link=]]PEAKS==<br />
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] <br />
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]<br />
: Peaks for the rotation function (ROT) or translation function (TRA) satisfying selection criteria are saved<br />
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.<br />
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.<br />
: <sup>3</sup> Select peaks by taking top CUTOFF.<br />
: <sup>4</sup> Select all peaks.<br />
; PEAKS ROT CUTOFF <CUTOFF><br />
; PEAKS TRA CUTOFF <CUTOFF><br />
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.<br />
; PEAKS ROT CLUSTER [ON|OFF] <br />
; PEAKS TRA CLUSTER [ON|OFF]<br />
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).<br />
* Default: PEAKS ROT SELECT PERCENT<br />
* Default: PEAKS TRA SELECT PERCENT<br />
* Default: PEAKS ROT CUTOFF 75<br />
* Default: PEAKS TRA CUTOFF 75<br />
* Default: PEAKS ROT CLUSTER ON<br />
* Default: PEAKS TRA CLUSTER ON<br />
setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) <br />
setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])<br />
setPEAK_ROTA_CUTO(float <CUTOFF>)<br />
setPEAK_TRAN_CUTO(float <CUTOFF>) <br />
setPEAK_ROTA_CLUS(bool <CLUSTER>) <br />
setPEAK_TRAN_CLUS(bool <CLUSTER>)<br />
<br />
==[[Image:User2.gif|link=]]PERMUTATIONS== <br />
; PERMUTATIONS [ON|OFF]<br />
: Only relevant to [[#SEARCH | SEARCH MEHOD FULL]]. Toggle for whether the order of the search set is to be permuted.<br />
* Default: PERMUTATIONS OFF<br />
setPERM(bool <PERMUTATIONS>)<br />
<br />
==[[Image:User2.gif|link=]]PURGE== <br />
; PURGE ROT ENABLE [ON|OFF]<br />
; PURGE TRA ENABLE [ON|OFF]<br />
: Toggle for whether to purge the solution list from the RF or TF and after the refinement steps (in AUTO mode) according to the best solution found so far.<br />
; PURGE ROT PERCENT <PERC><br />
; PURGE TRA PERCENT <PERC><br />
: PERC is the percent of the difference between the top solution and the mean at which to purge the solutions.<br />
; PURGE ROT NUMBER <NUM><br />
; PURGE TRA NUMBER <NUM><br />
: NUM is the number of solutions to retain in purging. The number taken is the minimum of the number found with the PERCENT cutoff and the NUMBER cutoff. If NUM is zero then the number is not used as a selection criteria.<br />
* Default: PURGE ROT ENABLE ON PERC 75 NUM 0<br />
* Default: PURGE TRA ENABLE ON PERC 75 NUM 0<br />
setPURG_ROTA_ENAB(bool <ENABLE>)<br />
setPURG_TRAN_ENAB(bool <ENABLE>) <br />
setPURG_ROTA_PERC(float <PERC>) <br />
setPURG_TRAN_PERC(float <PERC>) <br />
setPURG_ROTA_NUMB(float <NUM>) <br />
setPURG_TRAN_NUMB(float <NUM>)<br />
<br />
==[[Image:User2.gif|link=]]RESOLUTION== <br />
; RESOLUTION HIGH <HIRES> <br />
: High resolution limit in Ångstroms. <br />
; RESOLUTION LOW <LORES><br />
: Low resolution limit in Ångstroms.<br />
; RESOLUTION AUTO HIGH <HIRES> <br />
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
; RESOLUTION AUTO LOW <LORES> <br />
: Low resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.<br />
* Default for molecular replacement: Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data<br />
* Default for experimental phasing: All data used<br />
setRESO_HIGH(float <HIRES>) <br />
setRESO_LOW(float <LORES>)<br />
setRESO_AUTO_HIGH(float <HIRES>) <br />
setRESO_AUTO_LOW(float <LORES>)<br />
setRESO(float <HIRES>,float <LORES>) <br />
setRESO_AUTO(float <HIRES>,float <LORES>)<br />
<br />
==[[Image:User2.gif|link=]]ROTATE== <br />
; ROTATE VOLUME FULL<br />
: Sample all unique angles <br />
; ROTATE AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> <br />
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER<br />
* Default: ROTATE VOLUME FULL<br />
setROTA_VOLU(string ["FULL"|"AROUND"|) <br />
setROTA_EULE(dvect3 <A B C>) <br />
setROTA_RANG(float <RANGE>)<br />
<br />
==[[Image:User2.gif|link=]]SCATTERING==<br />
; SCATTERING TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]<br />
: Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.<br />
; SCATTERING RESTRAINT [ON|OFF]<br />
: use Fdp restraints<br />
; SCATTERING SIGMA <SIGMA><br />
: Fdp restraint sigma used is SIGMA multiplied by initial fdp value<br />
* Default: SCATTERING SIGMA 0.2<br />
* Default: SCATTERING RESTRAINT ON<br />
addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) <br />
setSCAT_REST(bool) <br />
setSCAT_SIGM(float <SIGMA>)<br />
<br />
==[[Image:User2.gif|link=]]TNCS==<br />
; TNCS USE [ON|OFF]<br />
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)<br />
; TNCS REFINE ROTATION [ON | OFF]<br />
: Use TNCS correction method that includes a rotation refinement of the two TNCS related rotations (to separate the rotation function results) before the translation function<br />
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C><br />
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes (GRID OFF). Central value for grid search (GRID ON).<br />
; TNCS ROTATION GRID [ON | OFF]<br />
: Refine the initial rotation angle starting from a grid of orientations around the starting angle (default 0,0,0). Grid controlled by RANGE and SAMPLING. The best refined rotational angle will be selected.<br />
; TNCS ROTATION RANGE <angle><br />
: Maximum deviation from initial rotation from which to look for rotational deviation. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.<br />
; TNCS ROTATION SAMPLING <sampling><br />
: Sampling for rotation search. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.<br />
; TNCS TRA VECTOR <x y z> <br />
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.<br />
; TNCS VARIANCE RMSD <num><br />
: Input estimated rms deviation between pseudo-translational symmetry vector related molecules.<br />
; TNCS VARIANCE FRAC <num><br />
: Input estimated fraction of cell content that obeys pseudo-translational symmetry.<br />
; TNCS LINK RESTRAINT [ON | OFF]<br />
: Link the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS LINK SIGMA <sigma><br />
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing<br />
; TNCS PATT HIRES <hires><br />
: High resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT LORES <lores><br />
: Low resolution limit for Patterson calculation for TNCS detection<br />
; TNCS PATT PERCENT <percent><br />
: Percent of origin Patterson peak that qualifies as a TNCS vector<br />
; TNCS PATT DISTANCE <distance><br />
: Minium distance of Patterson peak from origin that qualifies as a TNCS vector<br />
; TNCS NMOL <NMOL><br />
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.<br />
* Default: TNCS USE ON<br />
* Default: TNCS REFINE ROTATION OFF<br />
* Default: TNCS ROTATION ANGLE 0 0 0<br />
* Default: TNCS ROTATION GRID ON<br />
* Default: TNCS ROTATION SAMPLING 0<br />
* Default: TNCS ROTATION RANGE 0<br />
* Default: TNCS VARIANCE RMS 0.4 <br />
* Default: TNCS VARIANCE FRAC 1 <br />
* Default: TNCS LINK RESTRAINT ON<br />
* Default: TNCS LINK SIGMA 0.1<br />
* Default: TNCS PATT HIRES 5<br />
* Default: TNCS PATT LORES 10<br />
* Default: TNCS PATT PERCENT 20<br />
* Default: TNCS PATT DISTANCE 15<br />
* Default: TNCS NMOL 2<br />
setTNCS_USE(bool)<br />
setTNCS_REFI_ROTA(bool)<br />
setTNCS_ROTA_ANGL(dvect3 <A B C>) <br />
setTNCS_ROTA_RANG(float <RANGE>) <br />
setTNCS_ROTA_SAMP(float <SAMPLING>)<br />
setTNCS_TRAN_VECT(dvect3 <X Y Z>) <br />
setTNCS_VARI_RMSD(float <RMSD>) <br />
setTNCS_VARI_FRAC(float <FRAC>)<br />
setTNCS_LINK_REST(bool)<br />
setTNCS_LINK_SIGM(float <SIGMA>) <br />
setTNCS_PATT_HIRE(float <HIRES>)<br />
setTNCS_PATT_LORE(float <LORES>) <br />
setTNCS_PATT_PERC(float <PERCENT>) <br />
setTNCS_PATT_DIST(float <DISTANCE>)<br />
setTNCS_NMOL(int <NMOL>)<br />
<br />
==[[Image:User2.gif|link=]]TRANSLATE== <br />
; TRANSLATE VOLUME [ <sup>1</sup>FULL| <sup>2</sup>REGION| <sup>3</sup>LINE | <sup>4</sup>AROUND ])<br />
: Search volume for brute force translation function.<br />
: <sup>1</sup> Cheshire cell or Primitive cell volume. <br />
: <sup>2</sup> Search along line. <br />
: <sup>3</sup> Search region.<br />
: <sup>4</sup> Search around a point.<br />
; <sup>1 2 3</sup>TRANSLATE START <X Y Z> <br />
; <sup>1 2 3</sup>TRANSLATE END <X Y Z><br />
: Search within region or line bounded by START and END.<br />
; <sup>4</sup>TRANSLATE POINT <X Y Z><br />
; <sup>4</sup>TRANSLATE RANGE <RANGE><br />
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.<br />
; TRANSLATE [ORTH | FRAC]<br />
: Coordinates are given in orthogonal or fractional values.<br />
* Default: TRANSLATE VOLUME FULL<br />
setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])<br />
setTRAN_START(dvect <START>)<br />
setTRAN_END(dvect <END>)<br />
setTRAN_POINT(dvect <POINT>)<br />
setTRAN_RANGE(float <RANGE>)<br />
setTRAN_FRAC(bool <True=FRAC False=ORTH>)<br />
<br />
==[[Image:User2.gif|link=]]ZSCORE== <br />
; ZSCORE USE [ON|OFF]<br />
: Use the TFZ tests. Only applicable with SEARCH METHOD FAST. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)<br />
; ZSCORE SOLVED <ZSCORE_SOLVED><br />
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. <br />
; ZSCORE HALF [ON|OFF]<br />
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)<br />
* Default: ZSCORE USE ON<br />
* Default: ZSCORE SOLVED 8<br />
* Default: ZSCORE HALF ON<br />
setZSCO_USE(bool <True=ON False=OFF>)<br />
setZSCO_SOLV(floatType ZSCORE_SOLVED)<br />
setZSCO_HALF(bool <True=ON False=OFF>)<br />
<br><br />
<br><br />
<br />
=Expert Keywords=<br />
==[[Image:Expert.gif|link=]]BOXSCALE==<br />
; BOXSCALE <BOXSCALE><br />
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE<br />
* Default: BOXSCALE 4<br />
setBOXS<float <BOXSCALE>)<br />
<br />
==[[Image:Expert.gif|link=]]MACANO== <br />
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for the refinement of SigmaN in the anisotropy correction<br />
; MACANO ANISO [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] ''{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}''<br />
: Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACANO PROTOCOL DEFAULT<br />
setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACMR== <br />
; MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of molecular replacement solutions<br />
; MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] ''SOLP [ON|OFF] LAST [ON|OFF} NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACMR PROTOCOL DEFAULT<br />
setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <SOLP>,bool <LAST>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACSAD== <br />
; MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for SAD refinement.<br />
:''n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details''<br />
; MACSAD K [ON|OFF] B [ON|OFF] SIGMA [ON|OFF] XYZ [ON|OFF] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [ON|OFF]} {NCYCLE <NCYC>} MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.<br />
*Default: MACSAD PROTOCOL DEFAULT<br />
setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACS(bool <K>,bool <nowiki><B></nowiki>,bool <SIGMA>,<br />
bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP><br />
bool <SA>,bool <SB>,bool <SP>,bool <SD>,<br />
bool <PK>, bool <PB>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]MACTNCS== <br />
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for pseudo-translational NCS refinement.<br />
; MACTNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] ''NCYCLE <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACTNCS PROTOCOL DEFAULT<br />
setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Expert.gif|link=]]NMAMETHOD== <br />
; NMAMETHOD OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>CA | <sup>3</sup>ALL ] <br />
: Define the atoms used for the normal mode analysis. <br />
: <sup>1</sup>Use the rotation-translation block method.<br />
: <sup>2</sup>Use C-alpha atoms only to determine the modes.<br />
: <sup>3</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). <br />
; NMAMETHOD MAXBLOCKS <MAXBLOCKS><br />
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.<br />
; NMAMETHOD NRES <NRES><br />
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. <br />
; NMAMETHOD RADIUS <RADIUS><br />
: Elastic Network Model interaction radius (Angstroms)<br />
; NMAMETHOD FORCE <FORCE><br />
: Elastic Network Model force constant<br />
* Default: NMAMETHOD OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1<br />
setNMAM_OSCI(str ["RTB"|"CA"|"ALL"])<br />
setNMAM_RTB_MAXB(float <MAXB>)<br />
setNMAM_RTB_NRES(float <NRES>) <br />
setNMAM_RADI(float <RADIUS>) <br />
setNMAM_FORC(float <FORCE>)<br />
<br />
==[[Image:Expert.gif|link=]]RESCORE== <br />
; RESCORE ROT [ON|OFF]<br />
; RESCORE TRA [ON|OFF]<br />
: Toggle for rescoring of fast rotation function (ROT) or fast translation function (TRA) search peaks. <br />
* Default: RESCORE ROT ON<br />
* Default: RESCORE TRA ON|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with search method [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.<br />
setRESC_ROTA(bool)<br />
setRESC_TRAN(bool)<br />
<br />
==[[Image:Expert.gif|link=]]RESHARPEN== <br />
; RESHARPEN PERCENTAGE <PERC><br />
: Perecentage of the B-factor in the direction of lowest fall-off (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps<br />
* Default: RESHARPEN PERCENT 100<br />
setRESH_PERC(float <PERCENT>)<br />
<br />
==[[Image:Expert.gif|link=]]SAMPLING==<br />
; SAMPLING ROT <SAMP><br />
; SAMPLING TRA <SAMP><br />
: Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.<br />
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (MODE = MR_BRF or MR_FRF)<br />
* Default: SAMP = dmin/5; (MODE = MR_BTF)<br />
* Default: SAMP = dmin/4; (MODE = MR_FTF)<br />
setSAMP_ROTA(float <SAMP>)<br />
setSAMP_TRAN(float <SAMP>)<br />
<br><br />
<br><br />
<br />
=Developer Keywords=<br />
==[[Image:Developer.gif|link=]]BINS== <br />
; BINS MIN <L> <br />
: The binning of the data. L = minimum number of bins.<br />
; BINS MAX <H> <br />
: The binning of the data. H = maximum number of bins.<br />
; BINS WIDTH <W><br />
: The binning of the data. W = width of the bins in number of reflections<br />
; BINS CUBIC <A> <nowiki><B></nowiki> <C><br />
: The binning of the data. A B C are the coefficients for the binning function A(S*S*S)+B(S*S)+CS where S = (1/resolution). Cubic coefficients restricted to monotonically increasing function: A >0, B >0, C >0 and either (a) A=B=0 or (b) A=0 or (c) B=0<br />
* Default: BINS MIN 6 MAX 50 WIDTH 500 CUBIC 0 1 0 <br />
setBINS_MINI(float <L>)<br />
setBINS_MAXI(float <H>)<br />
setBINS_WIDT(float <W>)<br />
setBINS_CUBI(dvect3 <A B C>)<br />
<br />
==[[Image:Developer.gif|link=]]BFACTOR==<br />
; BFACTOR WILSON RESTRAINT [ON|OFF]<br />
: Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.<br />
; BFACTOR SPHERICITY RESTRAINT [ON|OFF] <br />
: Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing<br />
; BFACTOR REFINE RESTRAINT [ON|OFF] <br />
: Toggle to use the restraint to zero for molecular Bfactor in molecular replacement.<br />
; BFACTOR WILSON SIGMA <SIGMA><br />
: The sigma of the Wilson restraint.<br />
; BFACTOR SPHERICITY SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
; BFACTOR REFINE SIGMA <SIGMA><br />
: The sigma of the sphericity restraint.<br />
* Default: BFACTOR WILSON RESTRAINT ON <br />
* Default: BFACTOR SPHERICITY RESTRAINT ON <br />
* Default: BFACTOR REFINE RESTRAINT ON <br />
* Default: BFACTOR WILSON SIGMA 5<br />
* Default: BFACTOR SPHERICITY SIGMA 5<br />
* Default: BFACTOR REFINE SIGMA 10<br />
setBFAC_WILS_REST(bool <True|False>)<br />
setBFAC_SPHE_REST(bool <True|False>)<br />
setBFAC_REFI_REST(bool <True|False>) <br />
setBFAC_WILS_SIGM(float <SIGMA>) <br />
setBFAC_SPHE_SIGM(float <SIGMA>) <br />
setBFAC_REFI_SIGM(float <SIGMA>)<br />
<br />
==[[Image:Developer.gif|link=]]CELL==<br />
; CELL <A> <nowiki><B></nowiki> <C> <ALPHA> <BETA> <GAMMA><br />
: Unit cell dimensions<br />
* Default: Cell read from MTZ file<br />
setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)<br />
setCELL6(float_array <A B C ALPHA BETA GAMMA>)<br />
<br />
==[[Image:Developer.gif|link=]]CLMN== <br />
; CLMN SPHERE <SPHERE><br />
: Radius for the decomposition of the Patterson in Ångstroms. If it is 0, the radius defaults to twice the mean radius of the ENSEMBLE.<br />
; CLMN LMIN <LMIN><br />
: Lower limit of L values.<br />
; CLMN LMAX <LMAX><br />
: Upper limit of L values. The largest L value used in the calculation is the minimum of LMAX and 2&pi; * SPHERE/dmin.<br />
* Default: CLMN LMIN 4<br />
* Default: CLMN LMAX 100<br />
* Default: CLMN SPHE 0<br />
setCLMN_SPHE(float <SPHERE>) <br />
setCLMN_LMIN(float <LMIN>) <br />
setCLMN_LMAX(float <LMAX>)<br />
<br />
==[[Image:Developer.gif|link=]]FFTS==<br />
; FFTS MIN <ATOMS_MIN> MAX <ATOMS_MAX><br />
: The minimum and maximum number of atoms of the range between which direct summation and fft methods are tested to see which is faster for structure factor and gradient calcuation (for this unit cell and resolution). For a number of atoms below ATOMS_MIN direct structure factor calculation is always used, and for a number of atoms above ATOMS_MAX ffts are always used for the structure factor calculation and the gradient calculations. Direct summation is always used for the curvatures. Use FFTS MIN 0 MAX O to always use ffts.<br />
* Default: FFTS MIN 20 MAX 80<br />
setFFTS_MINI(float <ATOMS_MIN>) <br />
setFFTS_MAXI(float <ATOMS_MAX>)<br />
<br />
==[[Image:Developer.gif|link=]]INTEGRATION==<br />
; INTEGRATION FIXED [ON|OFF]<br />
: Fix the number of integration points or determine the number of angular steps in the integration by the variance of the function<br />
; INTEGRATION STEP <STEP><br />
: Number of steps in angular integration of function if FIXED number of points<br />
* Default: INTEGRATION FIXED OFF<br />
setINTE_FIXE(bool <True|False>) <br />
setINTE_STEP(float <STEP>)<br />
<br />
==[[Image:Developer.gif|link=]]MACHL== <br />
; MACHL PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]<br />
: Protocol for refinement of Hendrickson-Lattman coefficients<br />
; MACHL COEF [ON|OFF] ''NCYCle <NCYC> MINIMIZER [BFGS|NEWTON|DESCENT]''<br />
: Macrocycle for custom refinement of Hendrickson-Lattman coefficients. Macrocycles are performed in the order in which they are entered.<br />
* Default: MACHL PROTOCOL DEFAULT<br />
setMACH_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])<br />
addMACH(bool <COEF>,<br />
int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])<br />
<br />
==[[Image:Developer.gif|link=]]NORMALIZATION==<br />
;NORMALIZATION BINS <B1 B2 ...> ANISO <HH> <KK> <LL> <HK> <HL> <KL> SOLK <SOLK> SOLB <SOLB><br />
: The normalization factors that correct for anisotropy in the data<br />
setNORM_BINS(float_array <B1 B2 ...>)<br />
setNORM_ANIS(dmat6 <HH KK LL HK HL KL>)<br />
setNORM_SOLK(float <SOLK>) <br />
setNORM_SOLB(float <SOLB>) <br />
setNORM(float_array <B1 B2 ...> ,dmat6 <HH KK LL HK HL KL>,float <SOLK>,float <SOLB>)<br />
<br />
==[[Image:Developer.gif|link=]]OUTLIER==<br />
; OUTLIER REJECT [ON|OFF]<br />
: Reject low probability data outliers<br />
; OUTLIER PROB <PROB><br />
: Cutoff for rejection of low probablity outliers<br />
* Default: OUTLIER REJECT ON PROB 0.000001<br />
setOUTL_REJE(bool) <br />
setOUTL_PROB(float <PROB>)<br />
<br />
==[[Image:Developer.gif|link=]]PTGROUP== <br />
; PTGROUP COVERAGE <COVERAGE><br />
: Percentage coverage for two sequences to be considered in same pointgroup<br />
; PTGROUP IDENTITY <IDENTITY><br />
: Percentage identity for two sequences to be considered in same pointgroup<br />
; PTGROUP RMSD <RMSD><br />
: Percentage rmsd for two models to be considered in same pointgroup<br />
; PTGROUP TOLERANCE ANGULAR <ANG><br />
: Angular tolerance for pointgroup<br />
; PTGROUP TOLERANCE SPATIAL <DIST><br />
: Spatial tolerance for pointgroup<br />
setPTGR_COVE(float <COVERAGE>) <br />
setPTGR_IDEN(float <IDENTITY>) <br />
setPTGR_RMSD(float <RMSD>) <br />
setPTGR_TOLE_ANGU(float <ANG>) <br />
setPTGR_TOLE_SPAT(float <DIST>)<br />
<br />
==[[Image:Developer.gif|link=]]SOLPARAMETERS==<br />
; SOLPARAMETERS FSOL <FSOL> BSOL <BSOL> FIXB [ON|OFF]<br />
: Babinet solvent parameters for Sigma(A) curves. If FIXB is OFF, then BSOL is calculated from FSOL using the formula BSOL = 99.1 + 5.79*exp(4.03*FSOL) from Glykos & Kokkinkdis Acta Cryst D56 p1070 (2000), otherwise BSOL is fixed at the input (or default) value.<br />
; SOLPARAMETERS RESTRAIN [ON|OFF]<br />
: Restrain the Babinet solvent parameters to the initial values during refinement.<br />
; SOLPARAMETERS RESOLUTION <HIRES><br />
; Do not apply Babinet solvent correction terms to resolutions higher than HIRES.<br />
* Default: SOLPARAMETERS FSOL 0.69 BSOL 378 FIXB ON<br />
* Default: SOLPARAMETERS RESTRAINT OFF<br />
* Default: SOLPARAMETERS RESOLUTION 0<br />
setSOLP_FSOL(float <FSOL>) <br />
setSOLP_BSOL(float <BSOL>)<br />
setSOLP_FIXB(bool) <br />
setSOLP_REST(bool)<br />
<br />
==[[Image:Developer.gif|link=]]SORT==<br />
; SORT [ON|OFF]<br />
: Sort the reflections into resolution order upon reading MTZ file, for performance gain in molecular replacement<br />
* Default: SORT ON<br />
setSORT(bool)<br />
<br />
==[[Image:Developer.gif|link=]]TARGET==<br />
; TARGET FRF [LERF1|LERF2|CROWTHER]<br />
: Target function for fast rotation searches (2)<br />
; TARGET FTF [LETF1|LETF2|CORRELATION]<br />
: Target function for fast translation searches (3)<br />
* Default: TARGET FRF LERF1 <br />
* Default: TARGET FTF LETF1<br />
setTARG_FRF(str ["LERF1"|"LERF2"|"CROWTHER"])<br />
setTARG_FTF(str ["LETF1"|"LETF2"|"CORRELATION"])<br />
<br />
==[[Image:Developer.gif|link=]]VARSAD==<br />
; VARSAD [ K <N> | B <N> | SIGMA <N> | SA <B1 B2 …> | SB <B1 B2 …> | SP <B1 B2 …> | SD <B1 B2 …> | PK <N> | PB <N>]<br />
: SAD variance parameters SA and SB (the real and imaginary components of Sigma Minus), SP (Sigma Plus) and SD (Sigma Delta) by resolution bin, the overall scale (K) and B-factor (B) for the anomalous scatterer model, the overall scale (PK) and B-factor (PB) for the partial structure (if given), and sigma-scale (SIGMA).<br />
setVARS(float_array <VARIANCES></div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser_Crystallographic_Software&diff=1513Phaser Crystallographic Software2012-06-27T16:17:48Z<p>WikiSysop: /* Currently Supported Releases */</p>
<hr />
<div>Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by [[Developers | Randy Read's group]] at the [http://www.cimr.cam.ac.uk Cambridge Insitute for Medical Research] (CIMR) in the [http://www.cam.ac.uk University of Cambridge] and is available through the [http://www.phenix-online.org Phenix] and [http://www.ccp4.ac.uk CCP4] software suites.<br />
<br />
This wiki supersedes http://www-structmed.cimr.cam.ac.uk/phaser/ which is now '''obsolete''' (and redirects to this page). A copy of the obsolete website can be found at http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/<br />
<br />
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. <br />
==Currently Supported Releases==<br />
====Phaser-2.5.1 <span style="color:darkorange">''Under Construction''</span>====<br />
:Download with Phenix Nightly Builds → [http://www.phenix-online.org/download/ Phenix Downloads]<br />
:Full Documentation → [[Phaser: Manual | Manual]]<br />
:Quicklinks to Keywords → [[Keywords | Keywords]]<br />
<br />
====Phaser-2.5.0====<br />
:Download with Phenix Official Release 1.8 (23rd June 2012)→ [http://www.phenix-online.org/download/ Phenix Downloads]<br />
:Download with CCP4 6.3 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.5: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|1466|Keywords}}<br />
<br />
====Phaser-2.3.0====<br />
:Download with CCP4 6.2 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.3: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|937|Keywords}}<br />
:Bugfixes<br />
:#Packing criteria incorrectly set for Phaser MR in CCP4i<br />
:#:''A fixed interface is available from the ftp site and replaces the distributed interface in automated downloads from 3rd August 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser_MR CCP4-6.2.0 interface bug]<br />
:# Released 32 bit binary occasionally aborts on 64 bit Linux <br />
:#: ''A fixed 32 bit binary is available from the ftp site and replaces the distributed binary in automated downloads from 19th October 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser CCP4-6.2.0 program bug].<br />
<br />
__NOTOC__<br />
<br />
==Referencing Phaser==<br />
Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.<br />
<br />
If you solve a structure with Phaser, please cite<br />
<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
<br />
<br />
__NOTOC__</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser_Crystallographic_Software&diff=1512Phaser Crystallographic Software2012-06-27T16:03:21Z<p>WikiSysop: /* Phaser-2.5.0 */</p>
<hr />
<div>Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by [[Developers | Randy Read's group]] at the [http://www.cimr.cam.ac.uk Cambridge Insitute for Medical Research] (CIMR) in the [http://www.cam.ac.uk University of Cambridge] and is available through the [http://www.phenix-online.org Phenix] and [http://www.ccp4.ac.uk CCP4] software suites.<br />
<br />
This wiki supersedes http://www-structmed.cimr.cam.ac.uk/phaser/ which is now '''obsolete''' (and redirects to this page). A copy of the obsolete website can be found at http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/<br />
<br />
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. <br />
==Currently Supported Releases==<br />
====Phaser-2.5.0====<br />
:Download with Phenix Official Release 1.8 (23rd June 2012)→ [http://www.phenix-online.org/download/ Phenix Downloads]<br />
:Download with CCP4 6.3 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.5: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|1466|Keywords}}<br />
<br />
====Phaser-2.3.0====<br />
:Download with CCP4 6.2 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.3: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|937|Keywords}}<br />
:Bugfixes<br />
:#Packing criteria incorrectly set for Phaser MR in CCP4i<br />
:#:''A fixed interface is available from the ftp site and replaces the distributed interface in automated downloads from 3rd August 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser_MR CCP4-6.2.0 interface bug]<br />
:# Released 32 bit binary occasionally aborts on 64 bit Linux <br />
:#: ''A fixed 32 bit binary is available from the ftp site and replaces the distributed binary in automated downloads from 19th October 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser CCP4-6.2.0 program bug].<br />
<br />
__NOTOC__<br />
<br />
==Referencing Phaser==<br />
Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.<br />
<br />
If you solve a structure with Phaser, please cite<br />
<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
<br />
<br />
__NOTOC__</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser_Crystallographic_Software&diff=1511Phaser Crystallographic Software2012-06-27T16:02:35Z<p>WikiSysop: /* Phaser-2.4.0 */</p>
<hr />
<div>Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by [[Developers | Randy Read's group]] at the [http://www.cimr.cam.ac.uk Cambridge Insitute for Medical Research] (CIMR) in the [http://www.cam.ac.uk University of Cambridge] and is available through the [http://www.phenix-online.org Phenix] and [http://www.ccp4.ac.uk CCP4] software suites.<br />
<br />
This wiki supersedes http://www-structmed.cimr.cam.ac.uk/phaser/ which is now '''obsolete''' (and redirects to this page). A copy of the obsolete website can be found at http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/<br />
<br />
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. <br />
==Currently Supported Releases==<br />
====Phaser-2.5.0====<br />
:Download with Phenix Official Release 1.8 → [http://www.phenix-online.org/download/ Phenix Downloads]<br />
:Download with CCP4 6.3 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.5: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|1466|Keywords}}<br />
<br />
====Phaser-2.3.0====<br />
:Download with CCP4 6.2 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.3: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|937|Keywords}}<br />
:Bugfixes<br />
:#Packing criteria incorrectly set for Phaser MR in CCP4i<br />
:#:''A fixed interface is available from the ftp site and replaces the distributed interface in automated downloads from 3rd August 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser_MR CCP4-6.2.0 interface bug]<br />
:# Released 32 bit binary occasionally aborts on 64 bit Linux <br />
:#: ''A fixed 32 bit binary is available from the ftp site and replaces the distributed binary in automated downloads from 19th October 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser CCP4-6.2.0 program bug].<br />
<br />
__NOTOC__<br />
<br />
==Referencing Phaser==<br />
Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.<br />
<br />
If you solve a structure with Phaser, please cite<br />
<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
<br />
<br />
__NOTOC__</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser_Crystallographic_Software&diff=1510Phaser Crystallographic Software2012-06-27T16:01:34Z<p>WikiSysop: /* Phaser-2.5.0 */</p>
<hr />
<div>Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by [[Developers | Randy Read's group]] at the [http://www.cimr.cam.ac.uk Cambridge Insitute for Medical Research] (CIMR) in the [http://www.cam.ac.uk University of Cambridge] and is available through the [http://www.phenix-online.org Phenix] and [http://www.ccp4.ac.uk CCP4] software suites.<br />
<br />
This wiki supersedes http://www-structmed.cimr.cam.ac.uk/phaser/ which is now '''obsolete''' (and redirects to this page). A copy of the obsolete website can be found at http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/<br />
<br />
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. <br />
==Currently Supported Releases==<br />
====Phaser-2.5.0====<br />
:Download with Phenix Official Release 1.8 → [http://www.phenix-online.org/download/ Phenix Downloads]<br />
:Download with CCP4 6.3 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.5: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|1466|Keywords}}<br />
<br />
====Phaser-2.4.0 ====<br />
:Download with Phenix Official Release 1.7.3-928 (6 Dec 2011) → [http://www.phenix-online.org/download/ Phenix Downloads]<br />
:Full Documentation → [[Phaser-2.4: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|977|Keywords}}<br />
:Bugfixes<br />
:#Heterogen atoms weren't carried through in PDB file in MR<br />
:#Packing function accepted cases where an ensemble with internal point group symmetry was on a special position <br />
:#:''Phaser-2.4.1''available since 8th December 2011<br />
<br />
====Phaser-2.3.0====<br />
:Download with CCP4 6.2 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.3: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|937|Keywords}}<br />
:Bugfixes<br />
:#Packing criteria incorrectly set for Phaser MR in CCP4i<br />
:#:''A fixed interface is available from the ftp site and replaces the distributed interface in automated downloads from 3rd August 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser_MR CCP4-6.2.0 interface bug]<br />
:# Released 32 bit binary occasionally aborts on 64 bit Linux <br />
:#: ''A fixed 32 bit binary is available from the ftp site and replaces the distributed binary in automated downloads from 19th October 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser CCP4-6.2.0 program bug].<br />
<br />
__NOTOC__<br />
<br />
==Referencing Phaser==<br />
Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.<br />
<br />
If you solve a structure with Phaser, please cite<br />
<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
<br />
<br />
__NOTOC__</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser_Crystallographic_Software&diff=1509Phaser Crystallographic Software2012-06-27T15:59:52Z<p>WikiSysop: </p>
<hr />
<div>Phaser is a program for phasing macromolecular crystal structures with maximum likelihood methods. It has been developed by [[Developers | Randy Read's group]] at the [http://www.cimr.cam.ac.uk Cambridge Insitute for Medical Research] (CIMR) in the [http://www.cam.ac.uk University of Cambridge] and is available through the [http://www.phenix-online.org Phenix] and [http://www.ccp4.ac.uk CCP4] software suites.<br />
<br />
This wiki supersedes http://www-structmed.cimr.cam.ac.uk/phaser/ which is now '''obsolete''' (and redirects to this page). A copy of the obsolete website can be found at http://www-structmed.cimr.cam.ac.uk/phaser_obsolete/<br />
<br />
Use the '''sidebar''' to navigate through the extensive documentation for Phaser. <br />
==Currently Supported Releases==<br />
====Phaser-2.5.0====<br />
:Download with Phenix Official Release 1.8 → [http://www.phenix-online.org/download/ Phenix Downloads]<br />
:Download with CCP4 6.3 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser: Manual | Manual]]<br />
:Quicklinks to Keywords → [[Keywords | Keywords]]<br />
<br />
====Phaser-2.4.0 ====<br />
:Download with Phenix Official Release 1.7.3-928 (6 Dec 2011) → [http://www.phenix-online.org/download/ Phenix Downloads]<br />
:Full Documentation → [[Phaser-2.4: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|977|Keywords}}<br />
:Bugfixes<br />
:#Heterogen atoms weren't carried through in PDB file in MR<br />
:#Packing function accepted cases where an ensemble with internal point group symmetry was on a special position <br />
:#:''Phaser-2.4.1''available since 8th December 2011<br />
<br />
====Phaser-2.3.0====<br />
:Download with CCP4 6.2 Package → [http://www.ccp4.ac.uk/download/ CCP4]<br />
:Full Documentation → [[Phaser-2.3: Manual | Manual]]<br />
:Quicklinks to Keywords → {{Oldid|937|Keywords}}<br />
:Bugfixes<br />
:#Packing criteria incorrectly set for Phaser MR in CCP4i<br />
:#:''A fixed interface is available from the ftp site and replaces the distributed interface in automated downloads from 3rd August 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser_MR CCP4-6.2.0 interface bug]<br />
:# Released 32 bit binary occasionally aborts on 64 bit Linux <br />
:#: ''A fixed 32 bit binary is available from the ftp site and replaces the distributed binary in automated downloads from 19th October 2011 onwards.'' → [http://www.ccp4.ac.uk/problems.php#6.2.0-phaser CCP4-6.2.0 program bug].<br />
<br />
__NOTOC__<br />
<br />
==Referencing Phaser==<br />
Citing crystallographic software in your paper is important for funding new software development. We rely on your citations to convince funding bodies that our software is being used.<br />
<br />
If you solve a structure with Phaser, please cite<br />
<br />
;Phaser crystallographic software [http://www.phaser.cimr.cam.ac.uk/images/b/b2/He5368.pdf pdf]<br />
: McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ.<br />
:J. Appl. Cryst. (2007). 40, 658-674.<br />
<br />
<br />
__NOTOC__</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.2:_Manual&diff=1508Phaser-2.2: Manual2012-06-27T15:58:18Z<p>WikiSysop: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.2. There are some changes between this version and previous versions so input scripts may need editing.<br />
<br />
==Keywords==<br />
Phaser can be run using CCP4-style keyword input<br />
;{{Oldid|499|Keyword Modes}}<br />
: The different functions that Phaser can perform and the keywords relevant for each mode <br />
;{{Oldid|500|Keywords}}<br />
: Detailed descriptions of the keywords<br />
;{{Oldid|501|Keyword Example Scripts}}<br />
: Copy and edit to start using Phaser from keyword input<br />
<br />
==Python==<br />
Phaser can be scripted using python. <br />
;{{Oldid|503|Python Run-Jobs}}<br />
: How to run Phaser from python and the functions relevant for each Run-Job<br />
;{{Oldid|504|Python Functions}}<br />
: Detailed descriptions of the functions <br />
;{{Oldid|505|Python Example Scripts}}<br />
: Copy and edit to start using Phaser from python<br />
<br />
==XML==<br />
There is XML output available for developers writing automation scripts.<br><br />
Please contact us for more information or XML output requests.<br />
;{{Oldid|506|XML}}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.5:_Manual&diff=1507Phaser-2.5: Manual2012-06-27T15:56:14Z<p>WikiSysop: </p>
<hr />
<div><div style="margin-left: 25px; float: right;">__NOTOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.5. There are some changes between this version and previous versions so input scripts may need editing. <br />
<br />
; {{Oldid|1464|Modes}}<br />
: The different functions that Phaser can perform and the keywords relevant for each mode<br />
; {{Oldid|805|Keyword Modes}}<br />
: Detailed descriptions of the keywords<br />
; {{Oldid|1441 | Keyword Example Scripts}}<br />
: Copy and edit to start using Phaser from keyword input<br />
; {{Oldid|1461| Python Example Scripts}}<br />
: Copy and edit to start using Phaser from python</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.4:_Manual&diff=1506Phaser-2.4: Manual2012-06-27T15:54:25Z<p>WikiSysop: /* XML */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.4. There are some changes between this version and previous versions so input scripts may need editing.<br />
<br />
==Keywords==<br />
Phaser can be run using CCP4-style keyword input<br />
;{{Oldid|805|Keyword Modes}}<br />
: The different functions that Phaser can perform and the keywords relevant for each mode <br />
;{{Oldid|977|Keywords}}<br />
: Detailed descriptions of the keywords<br />
;{{Oldid|737|Keyword Example Scripts}}<br />
: Copy and edit to start using Phaser from keyword input<br />
<br />
==Python==<br />
Phaser can be scripted using python. <br />
;{{Oldid|713|Python Run-Jobs}}<br />
: How to run Phaser from python and the functions relevant for each Run-Job<br />
;{{Oldid|938|Python Functions}}<br />
: Detailed descriptions of the functions <br />
;{{Oldid|601|Python Example Scripts}}<br />
: Copy and edit to start using Phaser from python<br />
<br />
==XML==<br />
There is XML output available for developers writing automation scripts.<br><br />
Please contact us for more information or XML output requests.<br />
;{{Oldid|506|XML}}</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.4:_Manual&diff=1505Phaser-2.4: Manual2012-06-27T15:54:12Z<p>WikiSysop: /* Python */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.4. There are some changes between this version and previous versions so input scripts may need editing.<br />
<br />
==Keywords==<br />
Phaser can be run using CCP4-style keyword input<br />
;{{Oldid|805|Keyword Modes}}<br />
: The different functions that Phaser can perform and the keywords relevant for each mode <br />
;{{Oldid|977|Keywords}}<br />
: Detailed descriptions of the keywords<br />
;{{Oldid|737|Keyword Example Scripts}}<br />
: Copy and edit to start using Phaser from keyword input<br />
<br />
==Python==<br />
Phaser can be scripted using python. <br />
;{{Oldid|713|Python Run-Jobs}}<br />
: How to run Phaser from python and the functions relevant for each Run-Job<br />
;{{Oldid|938|Python Functions}}<br />
: Detailed descriptions of the functions <br />
;{{Oldid|601|Python Example Scripts}}<br />
: Copy and edit to start using Phaser from python<br />
<br />
==XML==<br />
There is XML output available for developers writing automation scripts.<br><br />
Please contact us for more information or XML output requests.<br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=XML&oldid=506 XML]</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.4:_Manual&diff=1504Phaser-2.4: Manual2012-06-27T15:53:36Z<p>WikiSysop: /* Keywords */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.4. There are some changes between this version and previous versions so input scripts may need editing.<br />
<br />
==Keywords==<br />
Phaser can be run using CCP4-style keyword input<br />
;{{Oldid|805|Keyword Modes}}<br />
: The different functions that Phaser can perform and the keywords relevant for each mode <br />
;{{Oldid|977|Keywords}}<br />
: Detailed descriptions of the keywords<br />
;{{Oldid|737|Keyword Example Scripts}}<br />
: Copy and edit to start using Phaser from keyword input<br />
<br />
==Python==<br />
Phaser can be scripted using python. <br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Run-Jobs&oldid=713 Python Run-Jobs]<br />
: How to run Phaser from python and the functions relevant for each Run-Job<br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Functions&oldid=938 Python Functions]<br />
: Detailed descriptions of the functions <br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Example_Scripts&oldid=601 Python Example Scripts]<br />
: Copy and edit to start using Phaser from python<br />
<br />
==XML==<br />
There is XML output available for developers writing automation scripts.<br><br />
Please contact us for more information or XML output requests.<br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=XML&oldid=506 XML]</div>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=Phaser-2.4:_Manual&diff=1503Phaser-2.4: Manual2012-06-27T15:52:44Z<p>WikiSysop: /* Keywords */</p>
<hr />
<div><div style="margin-left: 25px; float: right;">__TOC__</div><br />
<br />
This is the documentation for Phaser&#8211;2.4. There are some changes between this version and previous versions so input scripts may need editing.<br />
<br />
==Keywords==<br />
Phaser can be run using CCP4-style keyword input<br />
; ((Oldid|805|Keyword Modes}}<br />
: The different functions that Phaser can perform and the keywords relevant for each mode <br />
; ((Oldid|977|Keywords}}<br />
: Detailed descriptions of the keywords<br />
; ((Oldid|737|Keyword Example Scripts}}<br />
: Copy and edit to start using Phaser from keyword input<br />
<br />
==Python==<br />
Phaser can be scripted using python. <br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Run-Jobs&oldid=713 Python Run-Jobs]<br />
: How to run Phaser from python and the functions relevant for each Run-Job<br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Functions&oldid=938 Python Functions]<br />
: Detailed descriptions of the functions <br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=Python_Example_Scripts&oldid=601 Python Example Scripts]<br />
: Copy and edit to start using Phaser from python<br />
<br />
==XML==<br />
There is XML output available for developers writing automation scripts.<br><br />
Please contact us for more information or XML output requests.<br />
;[http://www.phaser.cimr.cam.ac.uk/index.php?title=XML&oldid=506 XML]</div>WikiSysop