https://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&feed=atom&action=historySAD using CCP4i - Revision history2024-03-28T16:35:52ZRevision history for this page on the wikiMediaWiki 1.31.8https://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=2484&oldid=prevRandy: Describe the option of running ARP/wARP instead of buccaneer, which gives substantially better results in this case.2018-11-20T11:36:11Z<p>Describe the option of running ARP/wARP instead of buccaneer, which gives substantially better results in this case.</p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Only a quick build is carried out with Buccaneer.  If the result is substantially better with one hand than the other, set up a job to carry on building from that Buccaneer model.  You could use Buccaneer again, in which case you should open the Model Building module, choose "Buccaneer - autobuild/refine", start from experimental phases, provide the Buccaneer model from the Phaser pipeline, the corresponding Parrot MTZ file and the sequence.  Alternatively, you could use ARP/wARP Classic, in which case you should choose the same model but use the MTZ file produced for the correct hand by Phaser, set Refmac to use the Phased ML target and Rfree flags (both in "Required parameters") and make sure the HLA/B/C/D coefficients have been selected.  Five cycles of model-building (25 cycles in total) should be enough.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Only a quick build is carried out with Buccaneer.  If the result is substantially better with one hand than the other, set up a job to carry on building from that Buccaneer model.  You could use Buccaneer again, in which case you should open the Model Building module, choose "Buccaneer - autobuild/refine", start from experimental phases, provide the Buccaneer model from the Phaser pipeline, the corresponding Parrot MTZ file and the sequence.  Alternatively, you could use ARP/wARP Classic, in which case you should choose the same model but use the MTZ file produced for the correct hand by Phaser, set Refmac to use the Phased ML target and Rfree flags (both in "Required parameters") and make sure the HLA/B/C/D coefficients have been selected.  Five cycles of model-building (25 cycles in total) should be enough.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"># As an alternative, you could choose not to use Buccaneer in the original pipeline run, but rather to follow that by a run with ARP/wARP Classic, choosing the hand with better statistics in the parrot step.  When running ARP/wARP, select the option to use a different (pre-weighted) map and choose the parrot map coefficients (parrot.F_phi.F and parrot.F_phi.phi). Select the options to use the free R flag in Refmac, and to use the Phased ML target with the Hendrickson-Lattman coefficients from Phaser (i.e. HLA, HLB, HLC and HLD). Five cycles of model-building should again be enough.</ins></div></td></tr>
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</table>Randyhttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=2251&oldid=prevRandy: Suggest using Rfree flag in ARP/wARP, simplify how to specify HLA/B/C/D2016-04-09T15:44:55Z<p>Suggest using Rfree flag in ARP/wARP, simplify how to specify HLA/B/C/D</p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?  How many iodides were in the initial and final substructures?  How many were added?  Were any deleted?</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?  How many iodides were in the initial and final substructures?  How many were added?  Were any deleted?</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div># Only a quick build is carried out with Buccaneer.  If the result is substantially better with one hand than the other, set up a job to carry on building from that Buccaneer model.  You could use Buccaneer again, in which case you should open the Model Building module, choose "Buccaneer - autobuild/refine", start from experimental phases, provide the Buccaneer model from the Phaser pipeline, the corresponding Parrot MTZ file and the sequence.  Alternatively, you could use ARP/wARP Classic, in which case you should choose the same model but use the MTZ file produced for the correct hand by Phaser, set Refmac to use <del class="diffchange diffchange-inline">HL phase restraints </del>(in <del class="diffchange diffchange-inline">the Refmac tab</del>) and <del class="diffchange diffchange-inline">select </del>the HLA/B/C/D coefficients.  Five cycles of model-building (25 cycles in total) should be enough.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div># Only a quick build is carried out with Buccaneer.  If the result is substantially better with one hand than the other, set up a job to carry on building from that Buccaneer model.  You could use Buccaneer again, in which case you should open the Model Building module, choose "Buccaneer - autobuild/refine", start from experimental phases, provide the Buccaneer model from the Phaser pipeline, the corresponding Parrot MTZ file and the sequence.  Alternatively, you could use ARP/wARP Classic, in which case you should choose the same model but use the MTZ file produced for the correct hand by Phaser, set Refmac to use <ins class="diffchange diffchange-inline">the Phased ML target and Rfree flags </ins>(<ins class="diffchange diffchange-inline">both </ins>in <ins class="diffchange diffchange-inline">"Required parameters"</ins>) and <ins class="diffchange diffchange-inline">make sure </ins>the HLA/B/C/D coefficients <ins class="diffchange diffchange-inline">have been selected</ins>.  Five cycles of model-building (25 cycles in total) should be enough.</div></td></tr>
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</table>Randyhttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=1953&oldid=prevRandy: Add step to carry on building from very incomplete initial model2014-04-10T18:14:09Z<p>Add step to carry on building from very incomplete initial model</p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:14, 10 April 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?  How many iodides were in the initial and final substructures?  How many were added?  Were any deleted?</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?  How many iodides were in the initial and final substructures?  How many were added?  Were any deleted?</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"># Only a quick build is carried out with Buccaneer.  If the result is substantially better with one hand than the other, set up a job to carry on building from that Buccaneer model.  You could use Buccaneer again, in which case you should open the Model Building module, choose "Buccaneer - autobuild/refine", start from experimental phases, provide the Buccaneer model from the Phaser pipeline, the corresponding Parrot MTZ file and the sequence.  Alternatively, you could use ARP/wARP Classic, in which case you should choose the same model but use the MTZ file produced for the correct hand by Phaser, set Refmac to use HL phase restraints (in the Refmac tab) and select the HLA/B/C/D coefficients.  Five cycles of model-building (25 cycles in total) should be enough.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
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</table>Randyhttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=1723&oldid=prevRandy: formatting2013-04-11T21:51:51Z<p>formatting</p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 21:51, 11 April 2013</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look at the "Final phasing statistics" table at the end of the logfile.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look at the "Final phasing statistics" table at the end of the logfile.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* There is some explanation on important logfile sections in the Phaser Wiki</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* There is some explanation on important logfile sections in the Phaser Wiki</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?  How many iodides were in the initial and final substructures?  How many were added <del class="diffchange diffchange-inline">and</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?  How many iodides were in the initial and final substructures?  How many were added<ins class="diffchange diffchange-inline">?  Were any </ins>deleted?</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>deleted?</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Tutorial]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Tutorial]]</div></td></tr>
</table>Randyhttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=1722&oldid=prevRandy: A few more changes to match the current SAD pipeline.2013-04-11T21:25:09Z<p>A few more changes to match the current SAD pipeline.</p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 21:25, 11 April 2013</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7" >Line 7:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This tutorial demonstrates SAD phasing using the Phaser pipeline.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>This tutorial demonstrates SAD phasing using the Phaser pipeline.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Lysozyme will readily crystallise from a wide range of conditions and yield several crystal forms. One of those, tetragonal lysozyme, is particularly well suited for halide soaking, since it grows from a high concentration of sodium chloride. A dataset has been collected from a lysozyme crystal soaked in 0.5 M potassium iodide. A strong anomalous signal has been detected, and locations of anomalous scatterers have <ins class="diffchange diffchange-inline">already </ins>been found<ins class="diffchange diffchange-inline">, but you can</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Lysozyme will readily crystallise from a wide range of conditions and yield several crystal forms. One of those, tetragonal lysozyme, is particularly well suited for halide soaking, since it grows from a high concentration of sodium chloride. A dataset has been collected from a lysozyme crystal soaked in 0.5 M potassium iodide. A strong anomalous signal has been detected, and locations of anomalous scatterers have been found.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">choose optionally to look for them as part of this run</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Start the ccp4 GUI by typing ccp4i at the command line.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Start the ccp4 GUI by typing ccp4i at the command line.</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l19" >Line 19:</td>
<td colspan="2" class="diff-lineno">Line 19:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Make sure that "Mode for experimental phasing" is set to Single-wavelength anomalous dispersion (SAD). This is the default.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Make sure that "Mode for experimental phasing" is set to Single-wavelength anomalous dispersion (SAD). This is the default.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Note that Phaser requires F(+), SIGF(+), F(-) and SIGF(-) and not the FP and DANO used by some other programs.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Note that Phaser requires F(+), SIGF(+), F(-) and SIGF(-) and not the FP and DANO used by some other programs.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>#* <del class="diffchange diffchange-inline">Do not forget </del>to <del class="diffchange diffchange-inline">change </del>the <del class="diffchange diffchange-inline">"LLG-map calculation atom type" from the default Se to </del>I<del class="diffchange diffchange-inline">.</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>#* <ins class="diffchange diffchange-inline">If you are using SHELXD or HYSS </ins>to <ins class="diffchange diffchange-inline">determine </ins>the <ins class="diffchange diffchange-inline">initial substructure, a good number of </ins>I <ins class="diffchange diffchange-inline">atoms </ins>to <ins class="diffchange diffchange-inline">ask for would be 8</ins>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">#* In a general case one should set "Enantiomorph choice" </del>to <del class="diffchange diffchange-inline">Both enantiomorphs</del>. <del class="diffchange diffchange-inline">Why is this not necessary in this case?</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* It is also a good idea to fill in the TITLE.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* It is also a good idea to fill in the TITLE.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># When you have entered all the information, run Phaser.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># When you have entered all the information, run Phaser.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look at the "Final phasing statistics" table at the end of the logfile.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look at the "Final phasing statistics" table at the end of the logfile.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* There is some explanation on important logfile sections in the Phaser Wiki</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* There is some explanation on important logfile sections in the Phaser Wiki</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria<ins class="diffchange diffchange-inline">?  How many iodides were in the initial and final substructures?  How many were added and</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">deleted</ins>?</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Tutorial]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Tutorial]]</div></td></tr>
</table>Randyhttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=1721&oldid=prevRandy: Update to describe Phaser pipeline instead of old standalone Phaser-EP GUI2013-04-10T16:03:12Z<p>Update to describe Phaser pipeline instead of old standalone Phaser-EP GUI</p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:03, 10 April 2013</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>  Sequence file: hewl.pir</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>  Sequence file: hewl.pir</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This tutorial demonstrates SAD phasing <del class="diffchange diffchange-inline">starting from heavy atom positions </del>using Phaser.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This tutorial demonstrates SAD phasing using <ins class="diffchange diffchange-inline">the </ins>Phaser <ins class="diffchange diffchange-inline">pipeline</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l13" >Line 13:</td>
<td colspan="2" class="diff-lineno">Line 13:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Make a new project called "phaser_tute" using the Directories&ProjectDir button on the RHS of the GUI. Set the "Project" to "phaser_tute" and "uses directory" to the directory where the files for this tutorial are located, and make this the "Project for this session of the CCP4Interface". You will then be able to go directly to this directory in the GUI using the pull-down menu that appears before every file selection.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Make a new project called "phaser_tute" using the Directories&ProjectDir button on the RHS of the GUI. Set the "Project" to "phaser_tute" and "uses directory" to the directory where the files for this tutorial are located, and make this the "Project for this session of the CCP4Interface". You will then be able to go directly to this directory in the GUI using the pull-down menu that appears before every file selection.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Go to the Experimental Phasing module, in the yellow pull-down on the LHS of the GUI</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Go to the Experimental Phasing module, in the yellow pull-down on the LHS of the GUI</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div># <del class="diffchange diffchange-inline">Bring </del>up the GUI for Phaser</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div># <ins class="diffchange diffchange-inline">Open the Automated Search & Phasing tab, then bring </ins>up the GUI for <ins class="diffchange diffchange-inline">the Phaser SAD pipeline</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># You can choose (near the top) whether to use SHELXD (if you have the SHELX package installed) or HYSS (if you have the Phenix package installed) to find the substructure before running Phaser.  If not, you can use a predetermined substructure, such as the PDB file included with this tutorial.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"># You can also choose whether or not to run Parrot to carry out density modification and Buccaneer to carry out a very preliminary model building, in the pipeline after </ins>Phaser<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># All the yellow boxes need to be filled in.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># All the yellow boxes need to be filled in.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Make sure that "Mode for experimental phasing" is set to Single-wavelength anomalous dispersion (SAD). This is the default.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* Make sure that "Mode for experimental phasing" is set to Single-wavelength anomalous dispersion (SAD). This is the default.</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 26:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* There is some explanation on important logfile sections in the Phaser Wiki</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* There is some explanation on important logfile sections in the Phaser Wiki</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"># If you ran the whole pipeline, look at whether one hand gave better statistics than the other in the Parrot and Buccaneer steps.  Look at the better Buccaneer model in the corresponding Parrot map, using coot.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Tutorial]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Category:Tutorial]]</div></td></tr>
</table>Randyhttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=783&oldid=prevAirlie at 11:39, 12 August 20102010-08-12T11:39:24Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 11:39, 12 August 2010</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">All files </del>for this tutorial are <del class="diffchange diffchange-inline">distributed from the Phaser web page</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Data </ins>for this tutorial are <ins class="diffchange diffchange-inline">found [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials here]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>  Reflection data: iod_scala-unique.mtz</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>  Reflection data: iod_scala-unique.mtz</div></td></tr>
</table>Airliehttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=370&oldid=prevWikiSysop: add category2009-07-13T09:49:22Z<p>add category</p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 09:49, 13 July 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l24" >Line 24:</td>
<td colspan="2" class="diff-lineno">Line 24:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* There is some explanation on important logfile sections in the Phaser Wiki</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>#* There is some explanation on important logfile sections in the Phaser Wiki</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div># Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">#* Use the Phaser </del>[<del class="diffchange diffchange-inline">http</del>:<del class="diffchange diffchange-inline">//www-structmed.cimr.cam.ac.uk/phaser/documentation/phaser-2.1_key.html  documentation</del>]</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[<ins class="diffchange diffchange-inline">[Category</ins>:<ins class="diffchange diffchange-inline">Tutorial]</ins>]</div></td></tr>
</table>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=182&oldid=prevWikiSysop: Protected "SAD using CCP4i" ([edit=sysop] (indefinite) [move=sysop] (indefinite)) [cascading]2009-07-09T09:41:19Z<p>Protected "<a href="/index.php/SAD_using_CCP4i" title="SAD using CCP4i">SAD using CCP4i</a>" ([edit=sysop] (indefinite) [move=sysop] (indefinite)) [cascading]</p>
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<td colspan="1" style="background-color: #fff; color: #222; text-align: center;">Revision as of 09:41, 9 July 2009</td>
</tr><tr><td colspan="2" class="diff-notice" lang="en"><div class="mw-diff-empty">(No difference)</div>
</td></tr></table>WikiSysophttps://www.phaser.cimr.cam.ac.uk/index.php?title=SAD_using_CCP4i&diff=24&oldid=prevWikiSysop: Initialization from almanac2009-06-30T12:24:16Z<p>Initialization from almanac</p>
<p><b>New page</b></p><div>All files for this tutorial are distributed from the Phaser web page<br />
<br />
Reflection data: iod_scala-unique.mtz<br />
Heavy atom sites: iod_hyss_consensus_model.pdb<br />
Sequence file: hewl.pir<br />
<br />
This tutorial demonstrates SAD phasing starting from heavy atom positions using Phaser.<br />
<br />
<br />
Lysozyme will readily crystallise from a wide range of conditions and yield several crystal forms. One of those, tetragonal lysozyme, is particularly well suited for halide soaking, since it grows from a high concentration of sodium chloride. A dataset has been collected from a lysozyme crystal soaked in 0.5 M potassium iodide. A strong anomalous signal has been detected, and locations of anomalous scatterers have been found.<br />
<br />
# Start the ccp4 GUI by typing ccp4i at the command line.<br />
# Make a new project called "phaser_tute" using the Directories&ProjectDir button on the RHS of the GUI. Set the "Project" to "phaser_tute" and "uses directory" to the directory where the files for this tutorial are located, and make this the "Project for this session of the CCP4Interface". You will then be able to go directly to this directory in the GUI using the pull-down menu that appears before every file selection.<br />
# Go to the Experimental Phasing module, in the yellow pull-down on the LHS of the GUI<br />
# Bring up the GUI for Phaser<br />
# All the yellow boxes need to be filled in.<br />
#* Make sure that "Mode for experimental phasing" is set to Single-wavelength anomalous dispersion (SAD). This is the default.<br />
#* Note that Phaser requires F(+), SIGF(+), F(-) and SIGF(-) and not the FP and DANO used by some other programs.<br />
#* Do not forget to change the "LLG-map calculation atom type" from the default Se to I.<br />
#* In a general case one should set "Enantiomorph choice" to Both enantiomorphs. Why is this not necessary in this case?<br />
#* It is also a good idea to fill in the TITLE.<br />
# When you have entered all the information, run Phaser.<br />
# Look at the "Final phasing statistics" table at the end of the logfile.<br />
#* There is some explanation on important logfile sections in the Phaser Wiki<br />
# Look through the log file and identify the workflow. How many cycles did Phaser need to reach convergence? What are the convergence criteria?<br />
#* Use the Phaser [http://www-structmed.cimr.cam.ac.uk/phaser/documentation/phaser-2.1_key.html documentation]</div>WikiSysop