Keywords - Revision history

Randy: /* link=ENSEMBLE */ Add SERIAL part of key for specifying model number from ensemble file

2021-12-10T11:19:38Z

‎link=ENSEMBLE: Add SERIAL part of key for specifying model number from ensemble file

Randy: /* link=RFACTOR */ Change number to agree with code.

2021-06-24T08:37:08Z

‎link=RFACTOR: Change number to agree with code.

Randy: /* link=LLGMAPS */ More explanation of getting an initial map and what you see in a final LLG map.

2019-11-06T15:34:08Z

‎link=LLGMAPS: More explanation of getting an initial map and what you see in a final LLG map.

Randy: /* link=LLGCOMPLETE */ Explain how to get initial log-likelihood-gradient map

2019-11-06T15:24:32Z

‎link=LLGCOMPLETE: Explain how to get initial log-likelihood-gradient map

Randy: /* link=JOBS */ Update default for JOBS keyword

2019-07-16T08:10:41Z

‎link=JOBS: Update default for JOBS keyword

Randy: /* link=OUTLIER */ Document INFO subkey of OUTLIER command

2018-06-20T09:53:41Z

‎link=OUTLIER: Document INFO subkey of OUTLIER command

Randy: /* link=TRANSLATION */ Add setTRAN_PACK_NUMB command to Python section

2018-06-12T19:23:10Z

‎link=TRANSLATION: Add setTRAN_PACK_NUMB command to Python section

Randy: Add FIND defaults.

2018-04-30T13:10:00Z

Add FIND defaults.

Randy: /* link=TRANSLATION */ Clarify that full search should probably not be used.

2018-04-26T18:55:10Z

‎link=TRANSLATION: Clarify that full search should probably not be used.

Randy: /* link=TARGET */ Clarify regions searched for brute rotation and translation searches, and how those are specified.

2018-04-26T18:53:37Z

‎link=TARGET: Clarify regions searched for brute rotation and translation searches, and how those are specified.

@@ Line 102: / Line 102: @@
 ==[[Image:User1.gif|link=]]ENSEMBLE==
-; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL <NUM><sup>5</sup>''
+; ENSEMBLE <MODLID> [PDB|CIF] <PDBFILE> [RMS <RMS><sup>1</sup> | ID <ID><sup>2</sup> | CARD ON<sup>3</sup>] ''CHAIN "<CHAIN>"<sup>4</sup> MODEL SERIAL <NUM><sup>5</sup>''
 : The names of the PDB/CIF files used to build the ENSEMBLE, and either
 :: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure

@@ Line 902: / Line 902: @@
 ; RFACTOR CUTOFF <VALUE>
 : Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.
-* Default: RFACTOR USE ON CUTOFF 35
+* Default: RFACTOR USE ON CUTOFF 40
   setRFAC_USE(bool)
   setRFAC_CUTO(float <PERCENT>)

@@ Line 398: / Line 398: @@
 ==[[Image:Output.gif|link=]]LLGMAPS==
 ; LLGMAPS [ON|OFF]
-: Write log-likelihood gradient map coefficients to MTZ file
+: Write log-likelihood gradient map coefficients to MTZ file. Since these show features that have not yet been modelled in the substructure, they tend to be rather featureless at the end of substructure completion. To see the initial map before any sites have been included, note that you will have to set LLGCOMPLETE COMPLETE OFF.
 * Default: LLGMAPS OFF
   setLLGM(bool <True|False>)

@@ Line 491: / Line 491: @@
 ==[[Image:User2.gif|link=]]LLGCOMPLETE==
 ; LLGCOMPLETE COMPLETE [ON|OFF]
-: Toggle for structure completion by log-likelihood gradient maps
+: Toggle for structure completion by log-likelihood gradient maps. Set to OFF with LLGMAPS ON to get an initial log-likelihood-gradient map before any of the anomalous signal has been accounted for.
 ; LLGCOMPLETE SCATTERER <TYPE>
 : 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

@@ Line 200: / Line 200: @@
 ; JOBS <NUM>
 : Number of processors to use in parallelized sections of code
-* Default: JOBS 2
+* Default: JOBS 4
   setJOBS(int <NUM>)

@@ Line 1,083: / Line 1,083: @@
 ; OUTLIER PROB <PROB>
 : Cutoff for rejection of low probablity outliers
-* Default: OUTLIER REJECT ON PROB 0.000001
+; OUTLIER INFO <INFO>
   setOUTL_REJE(bool)
   setOUTL_PROB(float <PROB>)
 ==[[Image:Developer.gif|link=]]PTGROUP==

@@ Line 752: / Line 752: @@
   setTRAN_PACK_USE(bool)
   setTRAN_PACK_CUTO(float)
 ==[[Image:User2.gif|link=]]ZSCORE==

@@ Line 165: / Line 165: @@
 : Phassade, type of scatterers to find
 ; FIND NUMBER <NUMBER>
-: Phassade, number of scatteres to find
+: Phassade, number of scatterers to find
 ; FIND CLUSTER [ON|OFF]
 : Phassade, scatterer name is a cluster
@@ Line 176: / Line 176: @@
 ; FIND PURGE CUTOFF <CUTOFF>
 : Phassade, purge selection method cutoff after all Phassade FFT
   setFIND_SCAT(str <ATOMTYPE>)
   setFIND_NUMB(int <NUMBER>)

@@ Line 715: / Line 715: @@
 ; TRANSLATION VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])
 : Search volume for brute force translation function.
-: <sup>1</sup> Cheshire cell or Primitive cell volume.
+: <sup>1</sup> Cheshire cell or Primitive cell volume. There are probably no circumstances where this is better than carrying out a full fast translation search.
 : <sup>2</sup> Search region.
 : <sup>3</sup> Search along line.

@@ Line 697: / Line 697: @@
 ==[[Image:User2.gif|link=]]TARGET==
 ; TARGET ROT [FAST | BRUTE]
-: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.
+: Target function for fast rotation searches (2). BRUTE searches angles on a grid over a range specified by the ROTATE command, with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.
 ; TARGET TRA [FAST | BRUTE | PHASED]
-: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.
+: Target function for translation searches (3). BRUTE searches positions on a grid over a range specified by the TRANSLATION command, with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED selects the "phased translation function", for which a LABIN command should also be given, specifying FMAP, PHMAP and (optionally) FOM.
 * Default: TARGET ROT FAST
 * Default: TARGET TRA FAST