Difference between revisions of "PDB Web Services Script"
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(New page: == Overview == A short snippet of code utilizing the new PDB Web Services. == The Code == <source lang="python"> import pymol from pymol import stored, cmd import SOAPpy import string # ...) |
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== Overview == | == Overview == | ||
A short snippet of code utilizing the new PDB Web Services. | A short snippet of code utilizing the new PDB Web Services. | ||
| + | |||
| + | Notes: | ||
| + | # See [http://www.rcsb.org/robohelp/webservices/summary.htm PDB Web Services] | ||
| + | # You need [http://pywebsvcs.sourceforge.net/ SOAP for Python] installed | ||
| + | # 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. | ||
| + | # 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 == | == The Code == | ||
| Line 7: | Line 13: | ||
from pymol import stored, cmd | from pymol import stored, cmd | ||
import SOAPpy | import SOAPpy | ||
| − | |||
# define a mapping from three letters to one | # define a mapping from three letters to one | ||
| Line 24: | Line 29: | ||
# open up the PDB web services and make a connection | # open up the PDB web services and make a connection | ||
| − | stored.pyMOLSeq = | + | stored.pyMOLSeq = ''.join( stored.pyMOLSeq ) |
server = SOAPpy.SOAPProxy("http://www.pdb.org/pdb/services/pdbws") | server = SOAPpy.SOAPProxy("http://www.pdb.org/pdb/services/pdbws") | ||
# fetch the secondary structure assignment from the PDB & | # fetch the secondary structure assignment from the PDB & | ||
# split it up into an array of characters | # split it up into an array of characters | ||
| − | stored.ss = | + | stored.ss = list( server.getKabschSander("1foo", "A") ) |
# get the sequence | # get the sequence | ||
pdbSeq = server.getSequenceForStructureAndChain("1foo", "A") | pdbSeq = server.getSequenceForStructureAndChain("1foo", "A") | ||
| − | offset = | + | # danger: hackishly foolish, but worked for 1foo. |
| + | offset = pdbSeq.find( stored.pyMOLSeq ) | ||
# make the assignment in PyMOL | # make the assignment in PyMOL | ||
cmd.alter( "1foo and c. A and n. CA and i. " + str(offset) + "-", "ss=stored.ss.pop(0)" ) | cmd.alter( "1foo and c. A and n. CA and i. " + str(offset) + "-", "ss=stored.ss.pop(0)" ) | ||
| + | |||
| + | # show as cartoons | ||
| + | cmd.as("cartoon") | ||
</source> | </source> | ||
| + | |||
| + | [[Category:Script_Library]] | ||
| + | [[Category:UI_Scripts]] | ||
Latest revision as of 06:22, 26 January 2010
Overview
A short snippet of code utilizing the new PDB Web Services.
Notes:
- See PDB Web Services
- You need SOAP for Python installed
- 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.
- 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")