Difference between revisions of "BbPlane"

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(support multiple chains and proline)
(moved script to github)
 
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{{Infobox script-repo
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|type      = module
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|filename  = bbPlane.py
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|author    = [[User:Inchoate|Jason Vertrees]], [[User:Bell|Blaine Bell]] and [[User:Speleo3|Thomas Holder]]
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|license  = MIT
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}}
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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).
 
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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# 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):
 
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    """
 
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    Draws a plane across the backbone for a selection
 
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    PARAMS
 
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    objSel, 
 
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        (object or selection) protein object or selection
 
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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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    RETURNS
 
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    A new object representing the planes
 
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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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    * Avoid two-sided lighting until I rearrange the vertices
 
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    """
 
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    # format input
 
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    transp = float(transp)
 
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    stored.AAs = []
 
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    # need hydrogens
 
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    cmd.h_add(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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        cmd.iterate( obj + " and (" + objSel + ") and n. CA" , "stored.AAs.append('/"+obj+"/%s/%s/%s' % (segi,chain,resi))")
 
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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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        corners = [
 
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            curIdx + "/CA",
 
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            curIdx + "/O",
 
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            nextIdx + "/N extend 1 and e. H",
 
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            nextIdx + "/CA"
 
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            ]
 
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        # prolines
 
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        if cmd.count_atoms( "%s and resn PRO" % nextIdx ):
 
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            corners[2] = nextIdx + "/CD"
 
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        # if the data are incomplete for any residues, ignore
 
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        if map(cmd.count_atoms, corners) != [1,1,1,1]:
 
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            print 'peptide bond %s -> %s incomplete' % (curIdx, nextIdx)
 
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            continue
 
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        # populate the position array
 
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        pos = map(cmd.get_atom_coords, corners)
 
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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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        # fill in the vertex data for the triangles;
 
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        # two-sided lighting is an issue
 
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        obj.extend( [
 
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            VERTEX, pos[0][0], pos[0][1], pos[0][2],
 
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            VERTEX, pos[1][0], pos[1][1], pos[1][2],
 
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            VERTEX, pos[2][0], pos[2][1], pos[2][2],
 
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            VERTEX, pos[1][0], pos[1][1], pos[1][2],
 
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            VERTEX, pos[2][0], pos[2][1], pos[2][2],           
 
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            VERTEX, pos[3][0], pos[3][1], pos[3][2],
 
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            ])
 
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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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    newName =  cmd.get_unused_name("backbonePlane")
 
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    cmd.load_cgo(obj, newName)
 
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    cmd.set("cgo_transparency", transp, newName)
 
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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]]

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).

  • 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://pymolwiki.org/index.php?title=BbPlane&oldid=10569"