PDB Web Services Script

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Overview

A short snippet of code utilizing the new PDB Web Services.

Notes:

  1. See PDB Web Services
  2. You need SOAP for Python installed
  3. The sequence of a chain fetched from the PDB does not always equal the sequence of a chain fetched from the PDB Web Services. I believe the PDB Web Services has the complete biological chain, not just what's in the structure.
  4. The offset is a hack; it uses a trick in PyMOL and may not be robust at all. Use at your own caution.

The Code

import pymol
from pymol import stored, cmd
import SOAPpy
 
# define a mapping from three letters to one
# Thanks to whomever posted this on the PyMOLWiki:
#   http://www.pymolwiki.org/index.php/Label
one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \
'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y',    \
'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A',    \
'GLY':'G', 'PRO':'P', 'CYS':'C'}
 
# fetch some molecule; yes, 1foo exists in the PDB
cmd.fetch("1foo", async=0)
# get the sequence from PyMOL
stored.pyMOLSeq = []
cmd.iterate( "1foo and c. A and n. CA" , "stored.pyMOLSeq.append( one_letter[resn] )" )
 
# open up the PDB web services and make a connection
stored.pyMOLSeq = ''.join( stored.pyMOLSeq )
server = SOAPpy.SOAPProxy("http://www.pdb.org/pdb/services/pdbws")
 
# fetch the secondary structure assignment from the PDB &
# split it up into an array of characters
stored.ss = list( server.getKabschSander("1foo", "A") )
 
# get the sequence
pdbSeq = server.getSequenceForStructureAndChain("1foo", "A")
# danger: hackishly foolish, but worked for 1foo.
offset = pdbSeq.find( stored.pyMOLSeq )
 
# make the assignment in PyMOL
cmd.alter( "1foo and c. A and n. CA and i. " + str(offset) + "-", "ss=stored.ss.pop(0)" )
 
# show as cartoons
cmd.as("cartoon")
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