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Difference between revisions of "BbPlane"

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(multistate support, simplification of vertex ordering)
 
(moved script to github)
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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
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</source>
 
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= The Source =
 
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<source lang="python">
 
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#
 
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# -- bbPlane.py - draws a CGO plane across the backbone atoms of
 
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#                neighboring amino acids
 
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#
 
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# Author: Jason Vertrees, 06/2010
 
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#  Modified by Thomas Holder, 06/2010
 
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#  Modified by Blaine Bell, 08/2011
 
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# Copyright (C) Schrodinger
 
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# Open Source License: MIT
 
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#
 
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from pymol.cgo import *    # get constants
 
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from pymol import cmd, stored
 
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from chempy import cpv
 
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def bbPlane(objSel='(all)', color='white', transp=0.0, state=1, name=None, quiet=1):
 
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    """
 
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DESCRIPTION
 
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    Draws a plane across the backbone for a selection
 
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ARGUMENTS
 
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    objSel = string: protein object or selection {default: (all)}
 
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    color = string: color name or number {default: white}
 
−
 
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    transp = float: transparency component (0.0--1.0) {default: 0.0}
 
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    state = integer: object state, 0 for all states {default: 1}
 
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NOTES
 
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    You need to pass in an object or selection with at least two
 
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    amino acids.  The plane spans CA_i, O_i, N-H_(i+1), and CA_(i+1)
 
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    """
 
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    # format input
 
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    transp = float(transp)
 
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    state, quiet = int(state), int(quiet)
 
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    if name is None:
 
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        name = cmd.get_unused_name("backbonePlane")
 
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    if state < 0:
 
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        state = cmd.get_state()
 
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    elif state == 0:
 
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        for state in range(1, cmd.count_states(objSel)+1):
 
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            bbPlane(objSel, color, transp, state, name, quiet)
 
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        return
 
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    stored.AAs = []
 
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    coords = dict()
 
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    # need hydrogens on peptide nitrogen
 
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    cmd.h_add('(%s) and n. N' % objSel)
 
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    # get the list of residue ids
 
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    for obj in cmd.get_object_list(objSel):
 
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        sel = obj + " and (" + objSel + ")"
 
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        for a in cmd.get_model(sel + " and n. CA", state).atom:
 
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            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
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            stored.AAs.append(key)
 
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            coords[key] = [a.coord,None,None]
 
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        for a in cmd.get_model(sel + " and n. O", state).atom:
 
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            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
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            if key in coords:
 
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                coords[key][1] = a.coord
 
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        for a in cmd.get_model(sel + " and ((n. N extend 1 and e. H) or (r. PRO and n. CD))", state).atom:
 
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            key = '/%s/%s/%s/%s' % (obj,a.segi,a.chain,a.resi)
 
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            if key in coords:
 
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                coords[key][2] = a.coord
 
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    # need at least two amino acids
 
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    if len(stored.AAs) <= 1:
 
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        print "ERROR: Please provide at least two amino acids, the alpha-carbon on the 2nd is needed."
 
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        return
 
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    # prepare the cgo
 
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    obj = [
 
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        BEGIN, TRIANGLES,
 
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        COLOR,
 
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        ]
 
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    obj.extend(cmd.get_color_tuple(color))
 
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    for res in range(0, len(stored.AAs)-1):
 
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        curIdx, nextIdx = str(stored.AAs[res]), str(stored.AAs[res+1])
 
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        # populate the position array
 
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        pos = [coords[curIdx][0], coords[curIdx][1], coords[nextIdx][2], coords[nextIdx][0]]
 
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        # if the data are incomplete for any residues, ignore
 
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        if None in pos:
 
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            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
 
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            continue
 
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        if cpv.distance(pos[0], pos[3]) > 4.0:
 
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            print '%s and %s not adjacent' % (curIdx, nextIdx)
 
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            continue
 
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        # need to order vertices to generate correct triangles for plane
 
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        #      modified/added by B.Bell 8/18/2011
 
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        #      modified by Thomas Holder 2012
 
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        if cpv.dot_product(cpv.sub(pos[0], pos[1]), cpv.sub(pos[2], pos[3])) < 0:
 
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            vorder = [0,1,2,2,3,0]
 
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        else:
 
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            vorder = [0,1,2,3,2,1]
 
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        # fill in the vertex data for the triangles;
 
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        for i in vorder:
 
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            obj.append(VERTEX)
 
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            obj.extend(pos[i])
 
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    # finish the CGO
 
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    obj.append(END)
 
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    # update the UI
 
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    cmd.load_cgo(obj, name, state)
 
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    cmd.set("cgo_transparency", transp, name)
 
−
 
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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]]

Revision as of 12:28, 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).

  • Close up of planar atoms

  • A few more

  • Global view

Examples

# download the source and save as bbPlane.py
run bbPlane.py
fetch 1cll
# make planes for residues 4-9
bbPlane i. 4-10
Retrieved from "http://wiki.pymol.org/index.php?title=BbPlane&oldid=4249"