BbPlane

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Revision as of 15:34, 18 August 2011 by Bell (talk | contribs) (The order of the vertices needs to be sorted correctly to produce a correct plane for all sets of points)
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This script will draw a CGO plane between the backbone atoms of two neighboring residues. This is to show the planarity of the atoms. The image style this is meant to represent can be found many places, like "Introduction to Protein Structure" by Branden and Tooze (2nd ed. pp. 8).

Examples

# download the source and save as bbPlane.py
run bbPlane.py
fetch 1cll
# make planes for residues 4-9
bbPlane i. 4-10

The Source

#
# -- bbPlane.py - draws a CGO plane across the backbone atoms of
#                 neighboring amino acids
# 
# Author: Jason Vertrees, 06/2010
#   Modified by Thomas Holder, 06/2010
#   Modified by Blaine Bell, 08/2011
# Copyright (C) Schrodinger
# Open Source License: MIT
#
from pymol.cgo import *    # get constants
from pymol import cmd, stored
from chempy import cpv

def bbPlane(objSel='(all)', color='white', transp=0.0):
    """
DESCRIPTION
 
    Draws a plane across the backbone for a selection
 
ARGUMENTS
 
    objSel = string: protein object or selection {default: (all)}
 
    color = string: color name or number {default: white}
 
    transp = float: transparency component (0.0--1.0) {default: 0.0}
 
NOTES
 
    You need to pass in an object or selection with at least two
    amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
    """
    # format input
    transp = float(transp)
    stored.AAs = []
    coords = dict()
 
    # need hydrogens on peptide nitrogen
    cmd.h_add('(%s) and n. N' % objSel)
 
    # get the list of residue ids
    for obj in cmd.get_object_list(objSel):
        sel = obj + " and (" + objSel + ")"
        for a in cmd.get_model(sel + " and n. CA").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            stored.AAs.append(key)
            coords[key] = [a.coord,None,None]
        for a in cmd.get_model(sel + " and n. O").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            if key in coords:
                coords[key][1] = a.coord
        for a in cmd.get_model("(hydro or n. CD) and nbr. (" + sel + " and n. N)").atom:
            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
            if key in coords:
                coords[key][2] = a.coord
 
    # need at least two amino acids
    if len(stored.AAs) <= 1:
        print "ERROR: Please provide at least two amino acids, the alpha-carbon on the 2nd is needed."
        return
 
    # prepare the cgo
    obj = [
        BEGIN, TRIANGLES,
        COLOR,
        ]
    obj.extend(cmd.get_color_tuple(color))
 
    for res in range(0, len(stored.AAs)-1):
        curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
 
        # populate the position array
        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
 
        # if the data are incomplete for any residues, ignore
        if None in pos:
            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
            continue

        if cpv.distance(pos[0], pos[3]) > 4.0:
            print '%s and %s not adjacent' % (curIdx, nextIdx)
            continue

        # need to order vertices to generate correct triangles for plane
        #      modified/added by B.Bell 8/18/2011
        sumpos = cpv.add(pos[0], cpv.add(pos[1], cpv.add(pos[2], pos[3])))
        centerpos = [ sumpos[0]/4., sumpos[1]/4., sumpos[2]/4. ]
        angles = [ [ 0., 0 ] ]
        s00 = cpv.sub(pos[0], centerpos)
        for i in range(1,4):
            s = cpv.sub(pos[i], centerpos)
            ang = cpv.get_angle(s00, s)
            angles.append( [ ang, i] )
        def sortfirst(a, b):
            return cmp(a[0], b[0])
        angles.sort(sortfirst)
        verts = map(lambda x: x[1], angles)
        vorder = [ verts[0], verts[1], verts[2],
                   verts[2], verts[3], verts[1] ]
        # fill in the vertex data for the triangles; 
        for i in vorder:
            obj.append(VERTEX)
            obj.extend(pos[i])
            
    # finish the CGO
    obj.append(END)
 
    # update the UI
    newName =  cmd.get_unused_name("backbonePlane")
    cmd.load_cgo(obj, newName)
    cmd.set("cgo_transparency", transp, newName)
 
 
cmd.extend("bbPlane", bbPlane)