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Difference between revisions of "BbPlane"

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(support multiple chains and proline)
 
(improve speed, support two_sided_lighting)
Line 23: Line 23:
 
#  
 
#  
 
# Author: Jason Vertrees, 06/2010
 
# Author: Jason Vertrees, 06/2010
 +
#  Modified by Thomas Holder, 06/2010
 
# Copyright (C) Schrodinger
 
# Copyright (C) Schrodinger
 
# Open Source License: MIT
 
# Open Source License: MIT
Line 32: Line 33:
 
def bbPlane(objSel='(all)', color='white', transp=0.0):
 
def bbPlane(objSel='(all)', color='white', transp=0.0):
 
     """
 
     """
 +
DESCRIPTION
 +
 
     Draws a plane across the backbone for a selection
 
     Draws a plane across the backbone for a selection
  
    PARAMS
+
ARGUMENTS
     objSel
+
 
        (object or selection) protein object or selection
+
     objSel = string: protein object or selection {default: (all)}
  
 
     color = string: color name or number {default: white}
 
     color = string: color name or number {default: white}
Line 42: Line 45:
 
     transp = float: transparency component (0.0--1.0) {default: 0.0}
 
     transp = float: transparency component (0.0--1.0) {default: 0.0}
  
    RETURNS
+
NOTES
    A new object representing the planes
 
  
     NOTES
+
     You need to pass in an object or selection with at least two
    * 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)
 
     amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
 
    * Avoid two-sided lighting until I rearrange the vertices
 
 
 
     """
 
     """
 
     # format input
 
     # format input
 
     transp = float(transp)
 
     transp = float(transp)
 
     stored.AAs = []
 
     stored.AAs = []
 +
    coords = dict()
  
     # need hydrogens
+
     # need hydrogens on peptide nitrogen
     cmd.h_add(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):
         cmd.iterate( obj + " and (" + objSel + ") and n. CA" , "stored.AAs.append('/"+obj+"/%s/%s/%s' % (segi,chain,resi))")
+
         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(sel + " and ((n. N extend 1 and e. H) or (r. PRO and n. CD))").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
 
     # need at least two amino acids
Line 78: Line 89:
 
         curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
 
         curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
  
         corners = [
+
         # populate the position array
            curIdx + "/CA",
+
        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
            curIdx + "/O",
 
            nextIdx + "/N extend 1 and e. H",
 
            nextIdx + "/CA"
 
            ]
 
 
 
        # prolines
 
        if cmd.count_atoms( "%s and resn PRO" % nextIdx ):
 
            corners[2] = nextIdx + "/CD"
 
  
 
         # if the data are incomplete for any residues, ignore
 
         # if the data are incomplete for any residues, ignore
         if map(cmd.count_atoms, corners) != [1,1,1,1]:
+
         if None in pos:
 
             print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
 
             print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
 
             continue
 
             continue
 
        # populate the position array
 
        pos = map(cmd.get_atom_coords, corners)
 
  
 
         if cpv.distance(pos[0], pos[3]) > 4.0:
 
         if cpv.distance(pos[0], pos[3]) > 4.0:
Line 102: Line 102:
  
 
         # fill in the vertex data for the triangles;  
 
         # fill in the vertex data for the triangles;  
         # two-sided lighting is an issue
+
         for i in [0,1,2,3,2,1]:
        obj.extend( [
+
             obj.append(VERTEX)
            VERTEX, pos[0][0], pos[0][1], pos[0][2],
+
             obj.extend(pos[i])
            VERTEX, pos[1][0], pos[1][1], pos[1][2],
 
            VERTEX, pos[2][0], pos[2][1], pos[2][2],
 
 
 
             VERTEX, pos[1][0], pos[1][1], pos[1][2],
 
             VERTEX, pos[2][0], pos[2][1], pos[2][2],           
 
            VERTEX, pos[3][0], pos[3][1], pos[3][2],
 
            ])
 
  
 
     # finish the CGO
 
     # finish the CGO

Revision as of 11:52, 30 June 2010

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
# 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(sel + " and ((n. N extend 1 and e. H) or (r. PRO and n. CD))").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

        # fill in the vertex data for the triangles; 
        for i in [0,1,2,3,2,1]:
            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)