Difference between revisions of "BbPlane"

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{{Infobox script-repo
 +
|type      = module
 +
|filename  = bbPlane.py
 +
|author    = [[User:Inchoate|Jason Vertrees]], [[User:Bell|Blaine Bell]] and [[User:Speleo3|Thomas Holder]]
 +
|license  = MIT
 +
}}
 +
 
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).
 
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).
  
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# make planes for residues 4-9
 
# make planes for residues 4-9
 
bbPlane i. 4-10
 
bbPlane i. 4-10
</source>
 
 
= The Source =
 
<source lang="python">
 
#
 
# -- 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)
 
 
</source>
 
</source>
  
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[[Category:Math_Scripts]]
 
[[Category:Math_Scripts]]
 
[[Category:Structural_Biology_Scripts]]
 
[[Category:Structural_Biology_Scripts]]
 +
[[Category:Pymol-script-repo]]

Latest revision as of 08:28, 1 March 2012

Type Python Module
Download bbPlane.py
Author(s) Jason Vertrees, Blaine Bell and Thomas Holder
License MIT
This code has been put under version control in the project Pymol-script-repo

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