Difference between revisions of "ColorByRMSD"

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{{Infobox script-repo
 +
|type      = Python Module
 +
|filename  = colorbyrmsd.py
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|author    = [[User:Shiven|Shivender Shandilya]], [[User:Inchoate|Jason Vertrees]], [[User:Speleo3|Thomas Holder]]
 +
|license  = BSD-2-Clause
 +
}}
 +
 
== Introduction ==
 
== 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.
  
An attempt to perform a coloring of two structures by RMS deviation as calculated by PyMol's internal [[Rms_Cur]] command.
+
== Usage ==
  
== Code ==
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colorbyrmsd mobile, target [, doAlign [, doPretty [, guide [, method ]]]]
=== Shiven's Code ===
 
WARNING: This is still a work in progress, and is almost useless right now! It is just a proof of principle at this stage and mainly an attempt at using the "alignment" object to iterate over the aligned objects. However, if you make any improvements, please do edit this page to reflect the same.
 
  
<source lang="python">
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== Arguments ==
"""
 
--- ColorByRMSD: RMSD based coloring ---
 
Author  : Shivender Shandilya
 
Program : ColByRMS
 
Date    : July 2009
 
Version : 0.0.2 (very 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:
 
DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
 
----------------------------------------------------------------------
 
"""
 
 
import pymol
 
import cmd
 
 
# Code for a special case first
 
cmd.load("D:/PyMOL-1.2r1/data/tut/1hpv.pdb", "1hpv")
 
 
cmd.create("chA", "1hpv and polymer and chain A")
 
cmd.create("chB", "1hpv and polymer and chain B")
 
 
# We need the alignment object, but PyMol refuses to give us that unless
 
# we (needlessly) specify all the other values in the cmd.align() function
 
# all the 0's are needlessly forced to be specified...
 
# PyMol is not smart enough to use the defaults
 
cmd.align("chA and name CA", "chB and name CA",0,0,0,0,0,object="aln")
 
# So, lets use "super" instead
 
#cmd.super("chA", "chB",object="aln")
 
 
# Utter the magic word
 
cmd.refresh()
 
 
# Arrays to store all residue identifiers in "aln"
 
stored.alnAres = []
 
stored.alnBres = []
 
 
# Now interrogate "aln" to get residue numbers for each object
 
cmd.iterate("chA and aln","stored.alnAres.append(resi)")
 
cmd.iterate("chB and aln","stored.alnBres.append(resi)")
 
  
print "Length of alnAres: "+str(len(stored.alnAres))
+
* '''mobile''' = string: atom selection for mobile atoms
print "Length of alnBres: "+str(len(stored.alnBres))
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* '''target''' = string: atom selection for target atoms
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* '''doAlign''' = 0 or 1: Superpose selections before calculating distances {default: 1}
# The main function that assigns "cur_rms" as the new b-factor
+
* '''doPretty''' = 0 or 1: Show nice representation and colors {default: 1}
def colbyRMS(objA, alnAri, objB, alnBri):
+
* '''guide''' = 0 or 1: Only use C-alpha atoms {default: 1}
    cmd.alter(str(objA), "chain='Z'")
+
* '''method''' = align or super: Method to match atoms {default: super}
    cmd.alter(str(objB), "chain='Z'")
 
    cmd.rebuild()
 
    for x in range(len(alnAri)):
 
        rmsd = cmd.rms_cur(str(objA)+" and i. "+str(alnAri[x]), str(objB)+" and i. "+str(alnBri[x]), matchmaker=4)
 
        cmd.alter(str(objA)+" and resi "+str(alnAri[x]), "b = "+str(rmsd))
 
        cmd.alter(str(objB)+" and resi "+str(alnBri[x]), "b = "+str(rmsd))
 
 
cmd.extend("colbyRMS", colbyRMS)
 
 
# Run the just defined function
 
if len(stored.alnAres) > len(stored.alnBres):
 
    colbyRMS("chA",stored.alnAres,"chB",stored.alnBres)
 
else:
 
    colbyRMS("chB",stored.alnBres,"chA",stored.alnAres)
 
 
# Arrays to store the NEW b-factors
 
stored.alnAnb = []
 
stored.alnBnb = []
 
 
# Store the NEW b-factors
 
cmd.iterate("chA and aln","stored.alnAnb.append(b)")
 
cmd.iterate("chB and aln","stored.alnBnb.append(b)")
 
 
# Assign the just stored NEW b-factors to the original object
 
for x in range(len(stored.alnAres)):
 
    cmd.alter("1hpv and chain A and resi "+str(stored.alnAres[x]), "b = "+str(stored.alnAnb[x]))
 
for x in range(len(stored.alnBres)):
 
    cmd.alter("1hpv and chain B and resi "+str(stored.alnBres[x]), "b = "+str(stored.alnBnb[x]))
 
 
# Get rid of all intermediate objects etc.
 
cmd.delete("chA")
 
cmd.delete("chB")
 
cmd.delete("aln")
 
 
# Showcase what you did
 
cmd.orient()
 
cmd.hide("all")
 
cmd.show("cartoon", "1hpv")
 
cmd.cartoon("loop")
 
print "\n"
 
print "Colored by 'overall' RMSD...\n"
 
cmd.spectrum("b", "rainbow", "1hpv and polymer")
 
</source>
 
  
=== Jason's Attempt ===
+
== Examples ==
I decided to generalize what Shiven started into an actual function.  This code is based off Shiven's (above).
 
==== Examples ====
 
 
<source lang="python">
 
<source lang="python">
 
# example #1
 
# example #1
colorByRMSD 1cbs, 1hmt, doAlign=True, doPretty=T
+
colorbyrmsd 1cbs, 1hmt, doAlign=1, doPretty=1
 
# example #2
 
# example #2
colorByRMSD 1eaz, 1fao, doAlign=True, doPretty=T
+
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.
+
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">
+
[[Category:Script_Library]]
"""
+
[[Category:Structural_Biology_Scripts]]
--- ColorByRMSD: RMSD based coloring ---
+
[[Category:Pymol-script-repo]]
Author  : Shivender Shandilya, modified by Jason Vertrees
 
Program : ColByRMS
 
Date    : July 2009
 
Version : 0.0.2 (very 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:
 
DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
 
----------------------------------------------------------------------
 
"""
 
 
import pymol
 
import cmd
 
from pymol import stored
 
 
def strTrue(p):
 
    return p[0].upper() == "T"
 
 
# The main function that assigns "cur_rms" as the new b-factor
 
def rmsUpdateB(objA, alnAri, objB, alnBri):
 
    # don't need the *10 -- PyMOL scales things for us.
 
    for x in range(len(alnAri)):
 
        s1 = objA + " and n. CA and i. " + alnAri[x]
 
        s2 = objB + " and n. CA and i. " + alnBri[x]
 
        rmsd = cmd.rms_cur(s1, s2, matchmaker=4)
 
        cmd.alter( s1, "b = " + str(rmsd))
 
        cmd.alter( s2, "b = " + str(rmsd))
 
    cmd.sort(objA); cmd.sort(objB)
 
 
 
 
def colorByRMSD(objSel1, objSel2, doAlign="True", doPretty=None):
 
    """
 
    colorByRMSD -- align two structures and show the structural deviations in
 
        color to more easily see variable regions.
 
       
 
    PARAMS
 
   
 
        objSel1 (valid PyMOL object or selection)
 
            The first object to align. 
 
           
 
        objSel2 (valid PyMOL object or selection)
 
            The second object to align
 
           
 
        doAlign (boolean, either True or False)
 
            Should this script align your proteins or just leave them where they
 
            are?  If doAlign=True then your original proteins are aligned.  If
 
            doAlign=False, then they are not.  Regardless, the b-factors are
 
            changed.
 
            DEFAULT: True
 
           
 
        doPretty (boolean, either True or False)
 
            If doPretty=True then a simple representation is created to high-
 
            light the differences.  If False, then no change is done to the
 
            structure.
 
           
 
    RETURNS
 
        None.
 
       
 
    SIDE-EFFECTS
 
        Modified the b-factor columns in your original proteins.
 
       
 
    """
 
    # create backup copies; names starting with _ (underscores) are
 
    # hidden by PyMOL
 
    tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
 
   
 
    if strTrue(doAlign):
 
        # perform the alignment
 
        cmd.create( tObj1, objSel1 )
 
        cmd.create( tObj2, objSel2 )
 
        cmd.super( tObj1, tObj2, object=aln )
 
        # bug -- every other call undoes this...
 
        cmd.matrix_copy(tObj1, objSel1)
 
    else:
 
        # perform the alignment
 
        cmd.create( tObj1, objSel1 )
 
        cmd.create( tObj2, objSel2 )
 
        cmd.super( tObj1, tObj2, object=aln )
 
 
 
    cmd.alter( tObj1 + " or " + tObj2, "b=-10")
 
    cmd.alter( tObj1 + " or " + tObj2, "chain='A'")
 
    cmd.alter( tObj1 + " or " + tObj2, "segi='A'")
 
    # update PyMOL;
 
    # one of these should do the trick
 
    cmd.refresh(); cmd.rebuild(); cmd.sort(tObj1); cmd.sort(tObj2)
 
   
 
    #  Get the residue identifiers from the aln object
 
    stored.alnAres, stored.alnBres = [], []
 
    cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAres.append(resi)")
 
    cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBres.append(resi)")
 
 
 
    # reset the b-factors for each object
 
    rmsUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
 
 
 
    # Store the NEW b-factors
 
    stored.alnAnb, stored.alnBnb = [], []
 
    cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAnb.append(b)" )
 
    cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBnb.append(b)" )
 
 
 
    # Get rid of all intermediate objects etc.; clean up
 
    cmd.delete(tObj1)
 
    cmd.delete(tObj2)
 
    cmd.delete(aln)
 
   
 
    # Assign the just stored NEW b-factors to the original object
 
    for x in range(len(stored.alnAres)):
 
        cmd.alter(objSel1 + " and n. CA and i. " + str(stored.alnAres[x]), "b = " + str(stored.alnAnb[x]))
 
    for x in range(len(stored.alnBres)):
 
        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
 
        cmd.orient()
 
        cmd.hide("all")
 
        cmd.show_as("cartoon", objSel1 + " or " + objSel2)
 
        cmd.spectrum("b", 'rainbow',  "(" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )")
 
 
 
cmd.extend("colorByRMSD", colorByRMSD)
 
</source>
 

Latest revision as of 08:59, 16 March 2012

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