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(Created page with '== Acknowledgement == This script is based on the scaffold from ColorByRMSD. Peace love and harmomy goes to Shivender Shandilya and Jason Vertrees. == Introduction == This scrip…')
 
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== Acknowledgement ==
+
#REDIRECT [[colorbydisplacement]]
This script is based on the scaffold from ColorByRMSD. Peace love and harmomy goes to Shivender Shandilya and Jason Vertrees.
 
 
 
== Introduction ==
 
This script allows you to color two structures by distance displacement between a Open and Closed form of a protein, as calculated by PyMol's internal distance command. The pairwise, C-alpha or all-atom. . 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. With uncommenting/commenting it is possible to make Residues ''NOT'' used by [[Super]] for superposition, and hence for distance displacement calculation, colored ''white''.
 
 
 
== Code ==
 
Please use this script with the option '''doColor=T''' to print the coloring. Do keep in mind, all original B-factors values are overwritten!
 
There exist two versions. ColorByDisplacementCA is quick and is between CA atoms. Ideal for helices representation. ColorByDisplacementAll is between All atoms in residues and is quite slow => 3-5 mins for a run. Ideal for sticks representation.
 
 
 
 
 
==== Examples ====
 
<source lang="python">
 
# example #1
 
ColorByDisplacementCA O5NT, C5NT, doColor=T, doAlign=T, super1=resi 26-355, super2=resi 26-355
 
ColorByDisplacementAll O5NT, C5NT, doColor=T, doAlign=T, super1=resi 26-355, super2=resi 26-355
 
</source>
 
 
 
<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. 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. Residues not used for alignment are colored white.
 
</gallery>
 
 
 
<source lang="python">
 
"""
 
--- ColorByRMSD: RMSD based coloring ---
 
Authors : Shivender Shandilya; Jason Vertrees
 
Program : ColorByRMSD
 
Date    : July 2009
 
Version : 0.1.1
 
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 current RMSD as the new B-factor
 
def rmsUpdateB(objA, alnAri, objB, alnBri):
 
    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 as is?
 
            If doAlign=True then your original proteins are aligned.
 
            If 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
 
            highlight the differences.  If False, then no changes are made.
 
            DEFAULT: False
 
 
    RETURNS
 
        None.
 
 
    SIDE-EFFECTS
 
        Modifies the B-factor columns in your original structures.
 
 
    """
 
    # First create backup copies; names starting with __ (underscores) are
 
    # normally 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 )
 
        cmd.matrix_copy(tObj1, objSel1)
 
    else:
 
        # perform the alignment
 
        cmd.create( tObj1, objSel1 )
 
        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
 
    cmd.alter( objSel1 + " or " + objSel2, "b=-10")
 
    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)
 
 
    #  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)")
 
    cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBres.append(resi)")
 
 
    # Change 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 and clean up
 
    cmd.delete(tObj1)
 
    cmd.delete(tObj2)
 
    cmd.delete(aln)
 
 
    # Assign the just stored NEW B-factors to the original objects
 
    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)
 
 
 
    # Provide some useful information
 
    stored.allRMSDval = []
 
    stored.allRMSDval = stored.alnAnb + stored.alnBnb
 
    print "\nColorByRMSD completed successfully."
 
    print "The MINIMUM RMSD value is: "+str(min(stored.allRMSDval))
 
    print "The MAXIMUM RMSD value is: "+str(max(stored.allRMSDval))
 
 
 
    if doPretty!=None:
 
        # Showcase what we did
 
        cmd.orient()
 
        cmd.hide("all")
 
        cmd.show_as("cartoon", objSel1 + " or " + objSel2)
 
        # 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
 
        cmd.color("white", "notUsedForAln")
 
        # 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
 
        # If you would like to keep this selection intact,
 
        # just comment "cmd.delete" line and
 
        # uncomment the "cmd.disable" line below.
 
        cmd.delete("notUsedForAln")
 
        # cmd.disable("notUsedForAln")
 
 
 
        print "\nObjects are now colored by C-alpha RMS deviation."
 
        print "All residues with RMSD values greater than the maximum are colored white..."
 
 
cmd.extend("colorByRMSD", colorByRMSD)
 
</source>
 
 
 
[[Category:Script_Library]]
 
[[Category:Structural_Biology_Scripts]]
 

Latest revision as of 02:15, 28 March 2014