Modes - Revision history

Airlie: /* Normal Mode Analysis/SCEDS */

2016-09-05T12:23:45Z

‎Normal Mode Analysis/SCEDS

Airlie: /* Refinement and Phasing */

2016-09-05T12:22:13Z

‎Refinement and Phasing

Airlie: /* Automated Molecular Replacement */

2016-09-05T11:45:46Z

‎Automated Molecular Replacement

Airlie at 15:37, 7 March 2016

2016-03-07T15:37:46Z

Randy: /* Modes */ Add sample Python call to mode MR_ELLG

2015-11-25T14:51:36Z

‎Modes: Add sample Python call to mode MR_ELLG

Randy: /* Modes */ Add mode MR_ELLG

2015-11-25T14:48:29Z

‎Modes: Add mode MR_ELLG

Airlie: /* Keywords Relevant to Each Mode */ delete keyword table as it has never been maintained

2014-07-09T10:14:54Z

‎Keywords Relevant to Each Mode: delete keyword table as it has never been maintained

Airlie: /* Normal Mode Analysis/SCEDS */ NMAXYZ

2014-07-09T10:14:16Z

‎Normal Mode Analysis/SCEDS: NMAXYZ

Airlie: /* Refinement and Phasing */

2014-03-31T20:25:37Z

‎Refinement and Phasing

Airlie: /* Automated Molecular Replacement */ Wrap MR_GYRE mode into MR_AUTO with SEARCH METHOD GYRE

2013-12-16T11:06:37Z

‎Automated Molecular Replacement: Wrap MR_GYRE mode into MR_AUTO with SEARCH METHOD GYRE

@@ Line 71: / Line 71: @@
 ====Normal Mode Analysis/SCEDS====
-:; MODE NMAXYZ
+:; MODE NMA
-:Writes out coordinates of input structures that have been perturbed along normal modes, in a procedure similar to that described by Suhre & Sanejouand (Acta Cryst. D60, 796-799, 2004). Each run of the program writes out a matrix FILEROOT.mat that contains the eigenvectors and eigenvalues of the atomic Hessian, and can be read into subsequent runs of the same job, to speed up the analysis.
+:Writes out coordinates of input structures that have been perturbed along normal modes, in a procedure similar to that described by Suhre & Sanejouand (Acta Cryst. D60, 796-799, 2004). Perturbed coordinates are output in RMS increments for use in MR trials. Each run of the program writes out a matrix FILEROOT.mat that contains the eigenvectors and eigenvalues of the atomic Hessian, and can be read into subsequent runs of the same job, to speed up the analysis.
    ResultNMA r = runNMAXYZ(i=InputNMA)

@@ Line 40: / Line 40: @@
 :Combines the anisotropy correction, translational NCS analysis, and refinement against the likelihood function to optimize full or partial molecular replacement solutions and phase the data. At the end of refinement, the list of solutions is checked for duplicates, which are pruned
    ResultMR r = runMR_RNP(i=InputMR_RNP)
-:; MODE MR_GYRE
+:; MODE [http://www.jabberwocky.com/carroll/jabber/jabberwocky.html GYRE]
 :Combines the anisotropy correction, translational NCS analysis, and refinement against the likelihood function to optimize the rotations and relative translations (gyrations) between chains in an ensemble
    ResultGYRE r = runMR_GYRE(i=InputMR_RNP)
-:; MODE MR_OCC
+:; MODE [http://www.jabberwocky.com/carroll/jabber/jabberwocky.html GIMBLE]
-:Combines the anisotropy correction, translational NCS analysis, and occupancy refinement against the likelihood function to optimize the occupancies of residues. Occupancy refinement is performed for occupancies in sliding residue windows of a size determined by the expected LLG.
+:Combines the anisotropy correction, translational NCS analysis, and refinement against the likelihood function to optimize the rotations and translations between chains in an ensemble
    ResultMR r = runMR_OCC(i=InputMR_OCC)

@@ Line 18: / Line 18: @@
 :Two different search methods are available
 :: '''FAST''' ''Uses amalgamation to combine placements from a single translation function''
-:: '''FULL''' ''Heavily branched search without amalgamation''
+:: '''FULL''' ''Heavily branched search without amalgamation'''
    ResultMR r = runMR_AUTO(i=InputMR_AUTO)

@@ Line 41: / Line 41: @@
 :Combines the anisotropy correction, translational NCS analysis, and refinement against the likelihood function to optimize full or partial molecular replacement solutions and phase the data. At the end of refinement, the list of solutions is checked for duplicates, which are pruned
    ResultMR r = runMR_RNP(i=InputMR_RNP)
-:; MODE MR_RGR
+:; MODE MR_GYRE
 :Combines the anisotropy correction, translational NCS analysis, and refinement against the likelihood function to optimize the rotations and relative translations (gyrations) between chains in an ensemble
-   ResultMR r = runMR_RGR(i=InputMR_RNP)
+   ResultGYRE r = runMR_GYRE(i=InputMR_RNP)
 :; MODE MR_OCC
 :Combines the anisotropy correction, translational NCS analysis, and occupancy refinement against the likelihood function to optimize the occupancies of residues. Occupancy refinement is performed for occupancies in sliding residue windows of a size determined by the expected LLG.

@@ Line 66: / Line 66: @@
 :; MODE MR_ELLG
 :Determines the eLLG for any models defined as ensembles, reporting the eLLG at the full resolution of the data and the resolution predicted to reach the target LLG.
 ====Normal Mode Analysis/SCEDS====

@@ Line 36: / Line 36: @@
 :Determines whether molecular replacement solutions pack in the unit cell using a C-alpha clash test
    ResultMR r = runMR_PAK(i=InputMR_PAK)
 ====Refinement and Phasing====
 :; MODE MR_RNP
@@ Line 51: / Line 52: @@
 :Corrects the experimental data (amplitude and associated sigma) for anisotropy. First, the anisotropy is removed by scaling up data from weak directions and scaling down data from strong directions, preserving the overall equivalent isotropic B-factor.  Then (as suggested by Strong ''et al.'' (2006), PNAS 103:8060-8065), the data are resharpened to restore the original falloff in the strong direction.  The amount of resharpening can be controlled with the RESHARP keyword.
    ResultANO r = runANO(i=InputANO)
 ====Translational NCS and Twin analysis====
 :; MODE NCS
 :Finds pseudo-translational NCS vectors and corrects the data for intensity variations due to the ptNCS using likelihood methods. The data are corrected for anisotropy first and analysed for twinning before and after data correction.
    ResultNCS r = runNCS(i=InputNCS)
 ====Cell Content Analysis====
 :; MODE CCA
 :Determines the composition of the crystals using the "new" Matthews coefficients of Kantardjieff & Rupp (2003) ("Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA and protein-nucleic acid complex crystals". Protein Science 12:1865-1871). The molecular weight of ONE complex or assembly to be packed into the asymmetric unit is given and the possible Z values (number of copies of the complex or assembly) that will fit in the asymmetric unit and the relative frequency of their corresponding VM values is reported.
    ResultCCA r = runCCA(i=InputCCA)
 ====Normal Mode Analysis/SCEDS====
 :; MODE NMAXYZ

← Older revision		Revision as of 10:14, 9 July 2014
Line 76:		Line 76:
	:Combines automated molecular replacement with log-likelihood gradient completion to solve high resolution structures by single atom MR. The data are prepared with runMR_DAT and then the phasing is done withing the EP_AUTO mode.		:Combines automated molecular replacement with log-likelihood gradient completion to solve high resolution structures by single atom MR. The data are prepared with runMR_DAT and then the phasing is done withing the EP_AUTO mode.
	ResultEP r = runMR_ATOM(i=InputMR_ATOM)		ResultEP r = runMR_ATOM(i=InputMR_ATOM)
−
−	~~===Keywords Relevant to Each Mode===~~
−
−	~~{\| class="wikitable"~~
−	\|-
−	~~!Mode !! Relevant Keywords~~
−	\|-
−	~~! MR_AUTO~~
−	\| [[Keywords#BFACTOR \| BFACTOR]] [[Keywords#BINS \| BINS]] [[Keywords#BOXSCALE \| BOXSCALE]] [[Keywords#CELL \| CELL]] [[Keywords#CLMN \| CLMN]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#ELLG \| ELLG]] [[Keywords#ENSEMBLE \| ENSEMBLE]] [[Keywords#HKLIN \| HKLIN]] [[Keywords#HKLOUT \| HKLOUT]] [[Keywords#JOBS \| JOBS]] [[Keywords#KEYWORDS \| KEYWORDS]] [[Keywords#MACANO \| MACANO]] [[Keywords#MACMR \| MACMR]] [[Keywords#MACTNCS \| MACTNCS]] [[Keywords#MUTE \| MUTE]] [[Keywords#NORMALIZATION \| NORMALIZATION]] [[Keywords#OUTLIER \| OUTLIER]] [[Keywords#PACK \| PACK]] [[Keywords#PEAKS \| PEAK]] [[Keywords#PERMUTATIONS \| PERMUTATIONS]] [[Keywords#PTGROUP \| PTGROUP]] [[Keywords#PURGE \| PURGE]] [[Keywords#REFLECTIONS \| REFLECTIONS]] [[Keywords#RESCORE \| RESCORE]] [[Keywords#RESHARPEN \| RESHARPEN]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#RFACTOR \| RFACTOR]] [[Keywords#ROOT \| ROOT]] [[Keywords#ROTATE \| ROTATE]] [[Keywords#SAMPLING \| SAMPLING]] [[Keywords#SEARCH \| SEARCH]] [[Keywords#SGALTERNATIVE \| SGALTERNATIVE]] [[Keywords#SOLPARAMETERS \| SOLPARAMETERS]] [[Keywords#SOLUTION \| SOLUTION]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TARGET \| TARGET]] [[Keywords#TITLE \| TITLE]] [[Keywords#TNCS \| TNCS]] [[Keywords#TOPFILES \| TOPFILES]] [[Keywords#TRANSLATE \| TRANSLATE]] [[Keywords#VERBOSE \| VERBOSE]] [[Keywords#XYZOUT \| XYZOUT]] [[Keywords#ZSCORE \| ZSCORE]]
−	\|-
−	~~! MR_ROT~~
−	\| [[Keywords#BINS \| BINS]] [[Keywords#BOXSCALE \| BOXSCALE]] [[Keywords#CELL \| CELL]] [[Keywords#CLMN \| CLMN]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#ENSEMBLE \| ENSEMBLE]] [[Keywords#JOBS \| JOBS]] [[Keywords#KEYWORDS \| KEYWORDS]] [[Keywords#MACANO \| MACANO]] [[Keywords#MACTNCS \| MACTNCS]] [[Keywords#MUTE \| MUTE]] [[Keywords#NORMALIZATION \| NORMALIZATION]] [[Keywords#OUTLIER \| OUTLIER]] [[Keywords#PEAKS \| PEAKS]] [[Keywords#PURGE \| PURGE]] [[Keywords#REFLECTIONS \| REFLECTIONS]] [[Keywords#RESCORE \| RESCORE]] [[Keywords#RESHARPEN \| RESHARPEN]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#RFACTOR \| RFACTOR]] [[Keywords#ROOT \| ROOT]] [[Keywords#ROTATE \| ROTATE]] [[Keywords#SAMPLING \| SAMPLING]] [[Keywords#SEARCH \| SEARCH]] [[Keywords#SGALTERNATIVE \| SGALTERNATIVE]] [[Keywords#SOLPARAMETERS \| SOLPARAMETERS]] [[Keywords#SOLUTION \| SOLUTION]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TARGET \| TARGET]] [[Keywords#TITLE \| TITLE]] [[Keywords#TNCS \| TNCS]] [[Keywords#TOPFILES \| TOPFILES]] [[Keywords#VERBOSE \| VERBOSE]] [[Keywords#XYZOUT \| XYZOUT]]
−	\|-
−	~~! MR_TRA~~
−	\| [[Keywords#BINS \| BINS]] [[Keywords#BOXSCALE \| BOXSCALE]] [[Keywords#CELL \| CELL]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#ENSEMBLE \| ENSEMBLE]] [[Keywords#HKLIN \| HKLIN]] [[Keywords#HKLOUT \| HKLOUT]] [[Keywords#JOBS \| JOBS]] [[Keywords#KEYWORDS \| KEYWORDS]] [[Keywords#MACANO \| MACANO]] [[Keywords#MACTNCS \| MACTNCS]] [[Keywords#MUTE \| MUTE]] [[Keywords#NORMALIZATION \| NORMALIZATION]] [[Keywords#OUTLIER \| OUTLIER]] [[Keywords#PEAKS \| PEAKS]] [[Keywords#PTGROUP \| PTGROUP]] [[Keywords#PURGE \| PURGE]] [[Keywords#REFLECTIONS \| REFLECTIONS]] [[Keywords#RESCORE \| RESCORE]] [[Keywords#RESHARPEN \| RESHARPEN]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#RFACTOR \| RFACTOR]] [[Keywords#ROOT \| ROOT]] [[Keywords#SAMPLING \| SAMPLING]] [[Keywords#SEARCH \| SEARCH]] [[Keywords#SGALTERNATIVE \| SGALTERNATIVE]] [[Keywords#SOLPARAMETERS \| SOLPARAMETERS]] [[Keywords#SOLUTION \| SOLUTION]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TARGET \| TARGET]] [[Keywords#TITLE \| TITLE]] [[Keywords#TNCS \| TNCS]] [[Keywords#TOPFILES \| TOPFILES]] [[Keywords#TRANLATE \| TRANLATE]] [[Keywords#VERBOSE \| VERBOSE]] [[Keywords#XYZOUT \| XYZOUT]] [[Keywords#ZSCORE \| ZSCORE]]
−	\|-
−	~~! MR_RNP~~
−	\| [[Keywords#BFACTOR \| BFACTOR]] [[Keywords#BINS \| BINS]] [[Keywords#BOXSCALE \| BOXSCALE]] [[Keywords#CELL \| CELL]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#ENSEMBLE \| ENSEMBLE]] [[Keywords#HKLIN \| HKLIN]] [[Keywords#HKLOUT \| HKLOUT]] [[Keywords#JOBS \| JOBS]] [[Keywords#KEYWORDS \| KEYWORDS]] [[Keywords#MACANO \| MACANO]] [[Keywords#MACMR \| MACMR]] [[Keywords#MACTNCS \| MACTNCS]] [[Keywords#MUTE \| MUTE]] [[Keywords#NORMALIZATION \| NORMALIZATION]] [[Keywords#OUTLIER \| OUTLIER]] [[Keywords#PTGROUP \| PTGROUP]] [[Keywords#REFLECTIONS \| REFLECTIONS]] [[Keywords#RESHARPEN \| RESHARPEN]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#ROOT \| ROOT]] [[Keywords#SOLPARAMETERS \| SOLPARAMETERS]] [[Keywords#SOLUTION \| SOLUTION]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TITLE \| TITLE]] [[Keywords#TNCS \| TNCS]] [[Keywords#TOPFILES \| TOPFILES]] [[Keywords#VERBOSE \| VERBOSE]] [[Keywords#XYZOUT \| XYZOUT]]
−	\|-
−	~~! MR_PAK~~
−	\| [[Keywords#CELL \| CELL]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#ENSEMBLE \| ENSEMBLE]] [[Keywords#JOBS \| JOBS]] [[Keywords#KEYWORDS \| KEYWORDS]] [[Keywords#MUTE \| MUTE]] [[Keywords#PACK \| PACK]] [[Keywords#PTGROUP \| PTGROUP]] [[Keywords#ROOT \| ROOT]] [[Keywords#SOLUTION \| SOLUTION]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TITLE \| TITLE]] [[Keywords#TOPFILES \| TOPFILES]] [[Keywords#VERBOSE \| VERBOSE]] [[Keywords#XYZOUT \| XYZOUT]] [[Keywords#ZSCORE \| ZSCORE]]
−	\|-
−	~~! ANO~~
−	\| [[Keywords#BINS \| BINS]] [[Keywords#CELL \| CELL]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#HKLIN \| HKLNI]] [[Keywords#HKLOUT \| HKLOUT]] [[Keywords#MACANO \| MACANO]] [[Keywords#MUTE \| MUTE]] [[Keywords#NORMALIZATION \| NORMALIZATION]] [[Keywords#REFLECTIONS \| REFLECTIONS]] [[Keywords#RESHARPEN \| RESHARPEN]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#ROOT \| ROOT]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TITLE \| TITLE]] [[Keywords#VERBOSE \| VERBOSE]]
−	\|-
−	~~! CCA~~
−	\| [[Keywords#CELL \| CELL]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#MUTE \| MUTE]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#ROOT \| ROOT]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TITLE \| TITLE]] [[Keywords#VERBOSE \| VERBOSE]]
−	\|-
−	~~! NMA~~
−	\| [[Keywords#DEBUG \| DEBUG]] [[Keywords#EIGEN \| EIGEN]] [[Keywords#ENSEMBLE \| ENSEMBLE]] [[Keywords#JOBS \| JOBS]] [[Keywords#KEYWORDS \| KEYWORDS]] [[Keywords#MUTE \| MUTE]] [[Keywords#NMADOMAIN \| NMADOMAIN]] [[Keywords#NMAMETHOD \| NMAMETHOD]] [[Keywords#NMAPDB \| NMAPDB]] [[Keywords#ROOT \| ROOT]] [[Keywords#TITLE \| TITLE]] [[Keywords#VERBOSE \| VERBOSE]] [[Keywords#XYZOUT \| XYZOUT]]
−	\|-
−	~~! NCS~~
−	\| [[Keywords#BINS \| BINS]] [[Keywords#CELL \| CELL]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#HKLIN \| HKLIN]] [[Keywords#HKLOUT \| HKLOUT]] [[Keywords#JOBS \| JOBS]] [[Keywords#MACANO \| MACANO]] [[Keywords#MACTNCS \| MACTNCS]] [[Keywords#MUTE \| MUTE]] [[Keywords#NORMALIZATION \| NORMALIZATION]] [[Keywords#OUTLIER \| OUTLIER]] [[Keywords#REFLECTIONS \| REFLECTIONS]] [[Keywords#RESHARPEN \| RESHARPEN]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#ROOT \| ROOT]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TITLE \| TITLE]] [[Keywords#TNCS \| TNCS]] [[Keywords#VERBOSE \| VERBOSE]]
−	\|-
−	~~! EP_AUTO~~
−	\| [[Keywords#ATOM \| ATOM]] [[Keywords#BFACTOR \| BFACTOR]] [[Keywords#BINS \| BINS]] [[Keywords#CELL \| CELL]] [[Keywords#CLUSTER \| CLUSTER]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#CRYSTAL \| CRYSTAL]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#HAND \| HAND]] [[Keywords#HKLIN \| HKLIN]] [[Keywords#HKLOUT \| HKLOUT]] [[Keywords#JOBS \| JOBS]][[Keywords#KEYWORDS \| KEYWORDS]] [[Keywords#LLGCOMPLETE \| LLGCOMPLETE]] [[Keywords#LLGMAPS \| LLGMAPS]] [[Keywords#MACANO \| MACANO]] [[Keywords#MACSAD \| MACSAD]] [[Keywords#MACTNCS \| MACTNCS]] [[Keywords#MUTE \| MUTE]] [[Keywords#NORMALIZATION \| NORMALIZATION]] [[Keywords#OUTLIER \| OUTLIER]] [[Keywords#PARTIAL \| PARTIAL]] [[Keywords#RESHAPEN \| RESHAPEN]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#RFACTOR \| RFACTOR]] [[Keywords#ROOT \| ROOT]] [[Keywords#SCATTERING \| SCATTERING]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TITLE \| TITLE]] [[Keywords#TNCS \| TNCS]] [[Keywords#TOPFILES \| TOPFILES]] [[Keywords#VARSAD \| VARSAD]] [[Keywords#VERBOSE \| VERBOSE]] [[Keywords#WAVELENGTH \| WAVELENGTH]] [[Keywords#XYZOUT \| XYZOUT]]
−	\|-
−	~~! MR_ATOM~~
−	\| [[Keywords#ATOM \| ATOM]] [[Keywords#CELL \| CELL]] [[Keywords#COMPOSITION \| COMPOSITION]] [[Keywords#CRYSTAL \| CRYSTAL]] [[Keywords#DEBUG \| DEBUG]] [[Keywords#ELLG \| ELLG]] [[Keywords#ENSEMBLE \| ENSEMBLE]] [[Keywords#HKLIN \| HKLIN]] [[Keywords#HKLOUT \| HKLOUT]] [[Keywords#JOBS \| JOBS]] [[Keywords#KEYWORDS \| KEYWORDS]] [[Keywords#LLGCOMPLETE \| LLGCOMPLETE]] [[Keywords#LLGMAPS \| LLGMAPS]] [[Keywords#MACANO \| MACANO]] [[Keywords#MACMR \| MACMR]] [[Keywords#MACSAD \| MACSAD]] [[Keywords#MACTNCS \| MACTNCS]] [[Keywords#MUTE \| MUTE]] [[Keywords#NORMALIZATION \| NORMALIZATION]] [[Keywords#PACK \| PACK]] [[Keywords#PEAKS \| PEAKS]] [[Keywords#PERMUTATIONS \| PERMUTATIONS]] [[Keywords#PURGE \| PURGE]] [[Keywords#REFLECTIONS \| REFLECTIONS]] [[Keywords#RESCORE \| RESCORE]] [[Keywords#RESOLUTION \| RESOLUTION]] [[Keywords#RFACTOR \| RFACTOR]] [[Keywords#ROOT \| ROOT]] [[Keywords#SAMPLING \| SAMPLING]] [[Keywords#SEARCH \| SEARCH]] [[Keywords#SGALTERNATIVE \| SGALTERNATIVE]] [[Keywords#SOLUTION \| SOLUTION]] [[Keywords#SPACEGROUP \| SPACEGROUP]] [[Keywords#TITLE \| TITLE]] [[Keywords#TNCS \| TNCS]] [[Keywords#TOPFILES \| TOPFILES]] [[Keywords#VERBOSE \| VERBOSE]] [[Keywords#XYZOUT \| XYZOUT]] [[Keywords#ZSCORE \| ZSCORE]]
−	\|}