Difference between revisions of "BbPlane"

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m (The Source)
m (The Source)
Line 55: Line 55:
 
     stored.AAs = []
 
     stored.AAs = []
 
     coords = dict()
 
     coords = dict()
+
 
 
     # need hydrogens on peptide nitrogen
 
     # need hydrogens on peptide nitrogen
 
     cmd.h_add('(%s) and n. N' % objSel)
 
     cmd.h_add('(%s) and n. N' % objSel)
+
 
 
     # get the list of residue ids
 
     # get the list of residue ids
 
     for obj in cmd.get_object_list(objSel):
 
     for obj in cmd.get_object_list(objSel):
Line 74: Line 74:
 
             if key in coords:
 
             if key in coords:
 
                 coords[key][2] = a.coord
 
                 coords[key][2] = a.coord
+
 
 
     # need at least two amino acids
 
     # need at least two amino acids
 
     if len(stored.AAs) <= 1:
 
     if len(stored.AAs) <= 1:
 
         print "ERROR: Please provide at least two amino acids, the alpha-carbon on the 2nd is needed."
 
         print "ERROR: Please provide at least two amino acids, the alpha-carbon on the 2nd is needed."
 
         return
 
         return
+
 
 
     # prepare the cgo
 
     # prepare the cgo
 
     obj = [
 
     obj = [
Line 86: Line 86:
 
         ]
 
         ]
 
     obj.extend(cmd.get_color_tuple(color))
 
     obj.extend(cmd.get_color_tuple(color))
+
 
 
     for res in range(0, len(stored.AAs)-1):
 
     for res in range(0, len(stored.AAs)-1):
 
         curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
 
         curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
+
 
 
         # populate the position array
 
         # populate the position array
 
         pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
 
         pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
+
 
 
         # if the data are incomplete for any residues, ignore
 
         # if the data are incomplete for any residues, ignore
 
         if None in pos:
 
         if None in pos:
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             obj.append(VERTEX)
 
             obj.append(VERTEX)
 
             obj.extend(pos[i])
 
             obj.extend(pos[i])
           
+
         
 
     # finish the CGO
 
     # finish the CGO
 
     obj.append(END)
 
     obj.append(END)
+
 
 
     # update the UI
 
     # update the UI
 
     newName =  cmd.get_unused_name("backbonePlane")
 
     newName =  cmd.get_unused_name("backbonePlane")
 
     cmd.load_cgo(obj, newName)
 
     cmd.load_cgo(obj, newName)
 
     cmd.set("cgo_transparency", transp, newName)
 
     cmd.set("cgo_transparency", transp, newName)
+
 
 
 
cmd.extend("bbPlane", bbPlane)
 
cmd.extend("bbPlane", bbPlane)
 
</source>
 
</source>

Revision as of 11:45, 25 August 2011

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[1], verts[3], verts[2] ]
        # 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)