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{{Infobox script-repo
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|type      = Python Module
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|filename  = colorbyrmsd.py
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|author    = [[User:Shiven|Shivender Shandilya]], [[User:Inchoate|Jason Vertrees]], [[User:Speleo3|Thomas Holder]]
 +
|license  = BSD-2-Clause
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}}
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== Introduction ==
 
== Introduction ==
−
An attempt to perform a coloring of two structures by RMS deviation as calculated by PyMol's internal [[Rms_Cur]] command.
+
This script allows you to color two structures by Root Mean Square Deviation (RMSD).
 +
The distances between aligned C-alpha atom pairs are stored as B-factors of these residues, which are colored by a color spectrum, with blue specifying the minimum pairwise RMSD and red indicating the maximum.
 +
Unaligned residues are colored gray.
 +
 
 +
== Usage ==
 +
 
 +
colorbyrmsd mobile, target [, doAlign [, doPretty [, guide [, method ]]]]
 +
 
 +
== Arguments ==
  
−
== Code ==
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* '''mobile''' = string: atom selection for mobile atoms
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This is new code, modified from the work done by Jason and myself.<br>
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* '''target''' = string: atom selection for target atoms
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If you use the option '''doPretty=T''', the residues NOT used for alignment/superposition are now colored '''white'''.<br>
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* '''doAlign''' = 0 or 1: Superpose selections before calculating distances {default: 1}
−
Please test and see if it works (somewhat) better. ''--[[User:Shiven|shiven]] 19:38, 16 July 2009 (UTC)''
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* '''doPretty''' = 0 or 1: Show nice representation and colors {default: 1}
 +
* '''guide''' = 0 or 1: Only use C-alpha atoms {default: 1}
 +
* '''method''' = align or super: Method to match atoms {default: super}
  
−
==== Examples ====
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== Examples ==
 
<source lang="python">
 
<source lang="python">
 
# example #1
 
# example #1
−
colorByRMSD 1cbs, 1hmt, doAlign=True, doPretty=T
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colorbyrmsd 1cbs, 1hmt, doAlign=1, doPretty=1
 
# example #2
 
# example #2
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colorByRMSD 1eaz, 1fao, doAlign=True, doPretty=T
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colorbyrmsd 1eaz, 1fao, doAlign=1, doPretty=1
 
</source>
 
</source>
  
 
<gallery heights="300px" widths="300px">
 
<gallery heights="300px" widths="300px">
−
Image:ColorByRMSD_1cbs_1hmt.png|1cbs and 1hmt aligned and colored by RMSD.  Dark blue is good alignment, higher deviations are in orange/yellow/red.
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Image:ColorByRMSD_1cbs_1hmt.png|1cbs and 1hmt aligned and colored by RMSD.  Dark blue is good alignment, higher deviations are in orange/yellow/red. Residues not used for alignment are colored white.
−
Image:ColorByRMSD_1eaz_1fao.png|1eaz and 1fao aligned and colored by RMSD.  Dark blue is good alignment, higher deviations are in orange/yellow/red.
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Image:ColorByRMSD_1eaz_1fao.png|1eaz and 1fao aligned and colored by RMSD.  Dark blue is good alignment, higher deviations are in orange/yellow/red. Residues not used for alignment are colored white.
 
</gallery>
 
</gallery>
−
 
−
<source lang="python">
 
−
"""
 
−
--- ColorByRMSD: RMSD based coloring ---
 
−
Authors : Shivender Shandilya; Jason Vertrees
 
−
Program : ColorByRMS
 
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Date    : July 2009
 
−
Version : 0.0.3 (very alpha!)
 
−
Mail    : firstname.lastname@umassmed.edu
 
−
 
−
Keywords: color rms rmsd colorbyrms colorbyrmsd
 
−
----------------------------------------------------------------------
 
−
Reference:
 
−
This email from Warren - http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07078.html
 
−
Literature:
 
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DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
 
−
----------------------------------------------------------------------
 
−
"""
 
−
 
−
import pymol
 
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import cmd
 
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from pymol import stored
 
−
 
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def strTrue(p):
 
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    return p[0].upper() == "T"
 
−
 
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# The main function that assigns "cur_rms" as the new b-factor
 
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def rmsUpdateB(objA, alnAri, objB, alnBri):
 
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    # don't need the *10 -- PyMOL scales things for us.
 
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    for x in range(len(alnAri)):
 
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        s1 = objA + " and n. CA and i. " + alnAri[x]
 
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        s2 = objB + " and n. CA and i. " + alnBri[x]
 
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        rmsd = cmd.rms_cur(s1, s2, matchmaker=4)
 
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        cmd.alter( s1, "b = " + str(rmsd))
 
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        cmd.alter( s2, "b = " + str(rmsd))
 
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    cmd.sort(objA); cmd.sort(objB)
 
−
 
−
 
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def colorByRMSD(objSel1, objSel2, doAlign="True", doPretty=None):
 
−
    """
 
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    colorByRMSD -- align two structures and show the structural deviations in
 
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        color to more easily see variable regions.
 
−
 
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    PARAMS
 
−
 
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        objSel1 (valid PyMOL object or selection)
 
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            The first object to align. 
 
−
 
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        objSel2 (valid PyMOL object or selection)
 
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            The second object to align
 
−
 
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        doAlign (boolean, either True or False)
 
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            Should this script align your proteins or just leave them where they
 
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            are?  If doAlign=True then your original proteins are aligned.  If
 
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            doAlign=False, then they are not.  Regardless, the b-factors are
 
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            changed.
 
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            DEFAULT: True
 
−
 
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        doPretty (boolean, either True or False)
 
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            If doPretty=True then a simple representation is created to high-
 
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            light the differences.  If False, then no change is done to the
 
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            structure.
 
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            DEFAULT: None
 
−
 
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    RETURNS
 
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        None.
 
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    SIDE-EFFECTS
 
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        Modified the b-factor columns in your original proteins.
 
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    """
 
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    # create backup copies; names starting with _ (underscores) are
 
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    # hidden by PyMOL
 
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    tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
 
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    if strTrue(doAlign):
 
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        # perform the alignment
 
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        cmd.create( tObj1, objSel1 )
 
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        cmd.create( tObj2, objSel2 )
 
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#      cmd.align( tObj1, tObj2, object=aln )
 
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        cmd.super( tObj1, tObj2, object=aln )
 
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        # bug -- every other call undoes this...
 
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        cmd.matrix_copy(tObj1, objSel1)
 
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    else:
 
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        # perform the alignment
 
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        cmd.create( tObj1, objSel1 )
 
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        cmd.create( tObj2, objSel2 )
 
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#      cmd.align( tObj1, tObj2, object=aln )
 
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        cmd.super( tObj1, tObj2, object=aln )
 
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#  cmd.alter( tObj1 + " or " + tObj2, "b=-10")
 
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#  Now modify the B-factor columns of the original objects,
 
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#  so as to later identify the residues NOT used for alignment
 
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    cmd.alter( objSel1 + " or " + objSel2, "b=-10")
 
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    cmd.alter( tObj1 + " or " + tObj2, "chain='A'")
 
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    cmd.alter( tObj1 + " or " + tObj2, "segi='A'")
 
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    # update PyMOL;
 
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    # one of these should do the trick
 
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    cmd.refresh(); cmd.rebuild(); cmd.sort(tObj1); cmd.sort(tObj2)
 
−
 
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    #  Get the residue identifiers from the aln object
 
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    stored.alnAres, stored.alnBres = [], []
 
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    cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAres.append(resi)")
 
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    cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBres.append(resi)")
 
−
 
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    print "Length of alnAres using 'super': "+str(len(stored.alnAres))
 
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    print "Length of alnBres using 'super': "+str(len(stored.alnBres))
 
−
 
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    # reset the b-factors for each object
 
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    rmsUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
 
−
 
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    # Store the NEW b-factors
 
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    stored.alnAnb, stored.alnBnb = [], []
 
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    cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAnb.append(b)" )
 
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    cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBnb.append(b)" )
 
−
 
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    # Get rid of all intermediate objects etc.; clean up
 
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    cmd.delete(tObj1)
 
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    cmd.delete(tObj2)
 
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    cmd.delete(aln)
 
−
 
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    # Assign the just stored NEW b-factors to the original object
 
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    for x in range(len(stored.alnAres)):
 
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        cmd.alter(objSel1 + " and n. CA and i. " + str(stored.alnAres[x]), "b = " + str(stored.alnAnb[x]))
 
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    for x in range(len(stored.alnBres)):
 
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        cmd.alter(objSel2 + " and n. CA and i. " + str(stored.alnBres[x]), "b = " + str(stored.alnBnb[x]))
 
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    cmd.rebuild(); cmd.refresh(); cmd.sort(objSel1); cmd.sort(objSel2)
 
−
 
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    if doPretty!=None:
 
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        # Showcase what we did
 
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        cmd.orient()
 
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        cmd.hide("all")
 
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        cmd.show_as("cartoon", objSel1 + " or " + objSel2)
 
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        # Select the residues not used for alignment; they still have their B-factors as "-10"
 
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        cmd.select("notUsedForAln", "b < 0")
 
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        cmd.disable("notUsedForAln")
 
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# White-wash the residues not used for alignment
 
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cmd.color("white", "notUsedForAln")
 
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# Color the residues used for alignment according to their B-factors (RMSD values)
 
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        cmd.spectrum("b", 'rainbow',  "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
 
−
 
−
cmd.extend("colorByRMSD", colorByRMSD)
 
−
</source>
 
  
 
[[Category:Script_Library]]
 
[[Category:Script_Library]]
 
[[Category:Structural_Biology_Scripts]]
 
[[Category:Structural_Biology_Scripts]]
 +
[[Category:Pymol-script-repo]]

Latest revision as of 01:21, 28 March 2014

Type Python Module
Download colorbyrmsd.py
Author(s) Shivender Shandilya, Jason Vertrees, Thomas Holder
License BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

Introduction

This script allows you to color two structures by Root Mean Square Deviation (RMSD). The distances between aligned C-alpha atom pairs are stored as B-factors of these residues, which are colored by a color spectrum, with blue specifying the minimum pairwise RMSD and red indicating the maximum. Unaligned residues are colored gray.

Usage

colorbyrmsd mobile, target [, doAlign [, doPretty [, guide [, method ]]]]

Arguments

  • mobile = string: atom selection for mobile atoms
  • target = string: atom selection for target atoms
  • doAlign = 0 or 1: Superpose selections before calculating distances {default: 1}
  • doPretty = 0 or 1: Show nice representation and colors {default: 1}
  • guide = 0 or 1: Only use C-alpha atoms {default: 1}
  • method = align or super: Method to match atoms {default: super}

Examples

# example #1
colorbyrmsd 1cbs, 1hmt, doAlign=1, doPretty=1
# example #2
colorbyrmsd 1eaz, 1fao, doAlign=1, doPretty=1

  • 1cbs and 1hmt aligned and colored by RMSD. Dark blue is good alignment, higher deviations are in orange/yellow/red. Residues not used for alignment are colored white.

  • 1eaz and 1fao aligned and colored by RMSD. Dark blue is good alignment, higher deviations are in orange/yellow/red. Residues not used for alignment are colored white.

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