ColorByRMSD - Revision history

Pyadmin: 26 revisions

2014-03-28T01:21:06Z

26 revisions

Speleo3: rewrite of script and moved script to github

2012-03-16T12:59:56Z

rewrite of script and moved script to github

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Shiven: /* Code */ Formatting - pesky Tabs/Spaces !

2009-07-18T22:17:37Z

Code: Formatting - pesky Tabs/Spaces !

Shiven: /* Examples */ Formatting

2009-07-18T22:11:13Z

Examples: Formatting

Shiven: /* Code */ Formatting

2009-07-18T22:10:20Z

Code: Formatting

Shiven: /* Code */ Formatting

2009-07-18T22:09:29Z

Code: Formatting

Shiven: Print out RMSD ranges and some useful information.

2009-07-18T22:07:28Z

Print out RMSD ranges and some useful information.

Shiven: /* Introduction */

2009-07-17T02:17:23Z

Introduction

Shiven: /* Introduction */

2009-07-17T02:17:01Z

Introduction

Shiven: /* Code */

2009-07-17T01:55:58Z

Code

@@ Line 151: / Line 151: @@
          # Select the residues not used for alignment; they still have their B-factors as "-10"
          cmd.select("notUsedForAln", "b < 0")
-	 # White-wash the residues not used for alignment
+        # White-wash the residues not used for alignment
-	 cmd.color("white", "notUsedForAln")
+        cmd.color("white", "notUsedForAln")
-	 # Color the residues used for alignment according to their B-factors (RMSD values)
+        # Color the residues used for alignment according to their B-factors (RMSD values)
          cmd.spectrum("b", 'rainbow',  "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
          # Delete the selection of atoms not used for alignment

@@ Line 151: / Line 151: @@
          # Select the residues not used for alignment; they still have their B-factors as "-10"
          cmd.select("notUsedForAln", "b < 0")
-	  # White-wash the residues not used for alignment
+	 # White-wash the residues not used for alignment
-	  cmd.color("white", "notUsedForAln")
+	 cmd.color("white", "notUsedForAln")
-	  # Color the residues used for alignment according to their B-factors (RMSD values)
+	 # Color the residues used for alignment according to their B-factors (RMSD values)
          cmd.spectrum("b", 'rainbow',  "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
          # Delete the selection of atoms not used for alignment

@@ Line 151: / Line 151: @@
          # Select the residues not used for alignment; they still have their B-factors as "-10"
          cmd.select("notUsedForAln", "b < 0")
-	 # White-wash the residues not used for alignment
+	  # White-wash the residues not used for alignment
-	 cmd.color("white", "notUsedForAln")
+	  cmd.color("white", "notUsedForAln")
-	 # Color the residues used for alignment according to their B-factors (RMSD values)
+	  # Color the residues used for alignment according to their B-factors (RMSD values)
          cmd.spectrum("b", 'rainbow',  "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
          # Delete the selection of atoms not used for alignment

@@ Line 151: / Line 151: @@
          # Select the residues not used for alignment; they still have their B-factors as "-10"
          cmd.select("notUsedForAln", "b < 0")
-	# White-wash the residues not used for alignment
+	 # White-wash the residues not used for alignment
-	cmd.color("white", "notUsedForAln")
+	 cmd.color("white", "notUsedForAln")
-	# Color the residues used for alignment according to their B-factors (RMSD values)
+	 # Color the residues used for alignment according to their B-factors (RMSD values)
          cmd.spectrum("b", 'rainbow',  "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
          # Delete the selection of atoms not used for alignment

@@ Line 24: / Line 24: @@
 Program : ColorByRMSD
 Date    : July 2009
-Version : 0.1.0 (first release!)
+Version : 0.1.1
 Mail    : firstname.lastname@umassmed.edu
@@ Line 52: / Line 52: @@
          cmd.alter( s2, "b = " + str(rmsd))
      cmd.sort(objA); cmd.sort(objB)
-−
 def colorByRMSD(objSel1, objSel2, doAlign="True", doPretty=None):
@@ Line 100: / Line 100: @@
          cmd.create( tObj2, objSel2 )
          cmd.super( tObj1, tObj2, object=aln )
-−
      # Modify the B-factor columns of the original objects,
      # in order to identify the residues NOT used for alignment, later on
@@ Line 106: / Line 106: @@
      cmd.alter( tObj1 + " or " + tObj2, "chain='A'")
      cmd.alter( tObj1 + " or " + tObj2, "segi='A'")
-−
      # Update pymol internal representations; one of these should do the trick
      cmd.refresh(); cmd.rebuild(); cmd.sort(tObj1); cmd.sort(tObj2)
@@ Line 112: / Line 112: @@
      #  Create lists for storage
      stored.alnAres, stored.alnBres = [], []
-−
      #  Get the residue identifiers from the alignment object "aln"
      cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAres.append(resi)")
@@ Line 119: / Line 119: @@
      # Change the B-factors for EACH object
      rmsUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
-−
      # Store the NEW B-factors
      stored.alnAnb, stored.alnBnb = [], []
@@ Line 136: / Line 136: @@
          cmd.alter(objSel2 + " and n. CA and i. " + str(stored.alnBres[x]), "b = " + str(stored.alnBnb[x]))
      cmd.rebuild(); cmd.refresh(); cmd.sort(objSel1); cmd.sort(objSel2)
-−
      if doPretty!=None:
          # Showcase what we did
@@ Line 153: / Line 160: @@
          # uncomment the "cmd.disable" line below.
          cmd.delete("notUsedForAln")
          # cmd.disable("notUsedForAln")
 cmd.extend("colorByRMSD", colorByRMSD)
 </source>

← Older revision	Revision as of 01:21, 28 March 2014
(No difference)

@@ Line 1: / Line 1: @@
 == Introduction ==
-This script allows you to color two structures by Root Mean Square Deviation (RMSD), as calculated by PyMol's internal [[Rms_Cur]] command. The pairwise, C-alpha, RMSD is calculated only between those residues which are first used by PyMol's internal [[Super]] command to superpose the two structures. The RMSD values are stored as B-factors of these residues, which are colored by a ''rainbow'' color spectrum, with blue specifying the minimum pairwise RMSD and red indicating the maximum. Residues ''NOT'' used by [[Super]] for superposition and hence for RMSD calculation are colored ''white''.
+This script allows you to color two structures by Root Mean Square Deviation (RMSD), as calculated by PyMol's internal [[Rms_Cur]] command. The pairwise, C-alpha, RMSD is calculated only between those residues which are first used by PyMol's internal [[Super]] command to superpose the two structures. The RMSD values are stored as B-factors of these residues, which are colored by a ''rainbow'' color spectrum, with blue specifying the minimum pairwise RMSD and red indicating the maximum. Residues ''NOT'' used by [[Super]] for superposition, and hence for RMSD calculation, are colored ''white''.
 == Code ==

@@ Line 3: / Line 3: @@
 == Code ==
-Please use this script with the option '''doPretty=T''' to gain the most benefit. Additionally, setting [[Cartoon]] representation to ''loop'', with the command: <source lang="python"> cartoon loop </script> may help ease comparisons. Do keep in mind, all original B-factors values are overwritten!
+Please use this script with the option '''doPretty=T''' to gain the most benefit. Additionally, setting [[Cartoon]] representation to ''loop'', with the command: <source lang="python"> cartoon loop </source> may help ease comparisons. Do keep in mind, all original B-factors values are overwritten!
 ==== Examples ====