Keyword Example Scripts - Revision history

Randy: Clarify how to run keyword scripts from Windows.

2018-02-19T12:10:23Z

Clarify how to run keyword scripts from Windows.

2018-02-16T19:45:07Z

Add instructions about sourcing scripts.

2016-08-25T09:23:02Z

‎Building an Ensemble from Coordinates: Remove reference to non-existent table, and mention using Ensembler to trim NMR ensembles.

2015-01-13T12:12:02Z

‎Non-Automated Molecular Replacement: transfer general section from MR with a script

2014-07-18T09:15:07Z

‎Brute Translation Function: Mode MR_BTF deprecated from example script

2014-07-18T09:14:30Z

‎Brute Rotation Function: Mode MR_BRF deprecated from example script

2013-12-09T12:12:49Z

‎Brute Translation Function: Remove script for degenerate translation function, which is no longer supported.

2013-12-09T12:11:23Z

‎"rlist" Files: Remove discussion of degenerate translation search, which is no longer supported.

2013-12-09T12:09:55Z

‎"sol" Files: Remove discussion of degenerate 3DIM and 5DIM cases, no longer supported.

2012-08-01T21:34:46Z

‎Translational NCS Analysis

@@ Line 4: / Line 4: @@
 ;$prompt> phaser
 After printing the Phaser Banner, the Preprocessor will ask:
@@ Line 21: / Line 23: @@
 *START
-Alternatively, phaser can be run from command scripts as below. Note that when you have a full script in a file, starting with the command "phaser" (CCP4 version) or "phenix.phaser" (Phenix version), you can run the script with the "source" command, <i>e.g.</i>
+Alternatively, phaser can be run from command scripts as below. Note that, for Unix systems, when you have a full script in a file, starting with the command "phaser" (CCP4 version) or "phenix.phaser" (Phenix version), you can run the script with the "source" command, <i>e.g.</i>
 ;$prompt> source myscript.com
-if your script is in a file named "myscript.com".
+if your script is in a file named "myscript.com".  Alternatively, for both Unix and Windows environments, you can make a script containing just the Phaser keyword commands and use redirection to run Phaser, <i>i.e.</i>
 ==How to Define Models==

← Older revision		Revision as of 19:45, 16 February 2018
Line 21:		Line 21:
	*START		*START

−	Alternatively, phaser can be run from command scripts as below	+	Alternatively, phaser can be run from command scripts as below. Note that when you have a full script in a file, starting with the command "phaser" (CCP4 version) or "phenix.phaser" (Phenix version), you can run the script with the "source" command, <i>e.g.</i>
		+
		+	;$prompt> source myscript.com
		+
		+	if your script is in a file named "myscript.com".

@@ Line 34: / Line 34: @@
    ENSEmble mol2   PDB structure1.pdb IDENtity .44 PDB structure2.pdb IDENtity .39 PDB structure3.pdb IDENtity .35
 </pre>
-You have an NMR Ensemble as a model. There is no need to split the coordinates in the pdb file provided that the models are separated by MODEL and ENDMDL cards. In this case the sequence identity is not a good indication of the rms deviation of the structural coordinates to the target structure. You should use the RMS option; several test cases have succeeded where the ID was close to 100% with an RMS value of about 1.5Å (see table below).
+You have an NMR Ensemble as a model. There is no need to split the coordinates in the pdb file provided that the models are separated by MODEL and ENDMDL cards. In this case the sequence identity is not a good indication of the rms deviation of the structural coordinates to the target structure. You should use the RMS option; several test cases have succeeded where the ID was close to 100% with an RMS value of about 1.5Å.  Note that, for NMR ensembles in which not all of the structure is well-defined, it is important to trim off parts of the models that diverge significantly.  This can be done easily in Ensembler, with the trim=True option.
 <pre>
    ENSEmble mol3 PDB nmr.pdb RMS 1.5

@@ Line 184: / Line 184: @@
 ==Non-Automated Molecular Replacement==
 ===Fast Rotation Function===
 Example command script for fast rotation function to find the orientation of BETA.

@@ Line 311: / Line 311: @@
    phaser << eof
    TITLe beta BTF
-   MODE MR_BTF
+   MODE MR_FTF
    HKLIn beta_blip.mtz
    LABIn F=Fobs SIGF=Sigma

@@ Line 240: / Line 240: @@
    phaser << eof
    TITLe beta BRF
-   MODE MR_BRF
+   MODE MR_FRF
    HKLIn beta_blip.mtz
    LABIn F=Fobs SIGF=Sigma
@@ Line 255: / Line 256: @@
    phaser << eof
    TITLe beta BRF fine sampling
-   MODE MR_BRF
+   MODE MR_FRF
    HKLIn beta_blip.mtz
    LABIn F=Fobs SIGF=Sigma
@@ Line 269: / Line 271: @@
    eof
 </pre>
 ===Fast Translation Function===
 Example command script for finding the position of BETA after the rotation function has been run and the results output to the file beta_frf.rlist

@@ Line 320: / Line 320: @@
    eof
 </pre>
-Example command script for brute Translation function to find the position of BETA degenerate in X after the rotation function has been run
 ===Refinement and Phasing===
 Example command script to refine a set of solutions

@@ Line 152: / Line 152: @@
    SOLUtion TRIAl ENSEmble mol1 EULEr 8 36 92 SCORE 4.2
    SOLUtion TRIAl ENSEmble mol1 EULEr 48 87 10 SCORE 4.0
 </pre>

@@ Line 115: / Line 115: @@
 One copy of mol1 with known orientation and position (fractional coordinates)
-    SOLUtion 6DIM ENSEmble mol1 EULEr 17 20 32 FRACtional 0.12 0.05 0.74
-One copy of mol1 with known orientation only
+<pre>
-    SOLUtion 3DIM ENSEmble mol1 EULEr 17 20 32
+  SOLUtion 6DIM ENSEmble mol1 EULEr 17 20 32 FRACtional 0.12 0.05 0.74
-One copy of mol1 with known orientation and only the coordinates in 2 dimensions is known. The degenerate direction is defined as the direction perpendicular to the plane in which the position is given.
+</pre>
 If the rotation function and translation function for mol1 were very clear, then there will only be one type of 6DIM solution for mol1. If the rotation and translation functions for mol2 were then not clear, there will be a series of possible 6DIM solutions for mol2.

@@ Line 451: / Line 451: @@
    phaser << eof
    TITLe BETA-BLIP translational NCS analysis
-   MODE NCS  HKLIn beta_blip.mtz
+   MODE NCS
    LABIn F=Fobs SIGF=Sigma
    COMPosition PROTein SEQuence beta.seq NUM 1 #beta
@@ Line 458: / Line 459: @@
    eof
 </pre>
 ==Normal Mode Analysis==
 Do normal mode analysis, write out eigenfile and coordinates perturbed by default movements along mode 7 only. (If you only wanted to prepare the eigenfile but not coordinates, you could include the command "XYZOut OFF").