Difference between revisions of "ColorByDisplacement"

Latest revision as of 02:15, 28 March 2014

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Colorbydisplacement

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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]]

Difference between revisions of "ColorByDisplacement"

Latest revision as of 02:15, 28 March 2014

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