Pyadmin: 6 revisions

2014-03-28T02:00:28Z

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Newacct: /* The Code */

2010-01-26T10:22:50Z

The Code

Newacct at 10:22, 26 January 2010

2010-01-26T10:22:29Z

New page

== Overview ==
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 ==
<source lang="python">
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 = [ x for x in 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")
</source>

[[Category:Script_Library]]
[[Category:UI_Scripts]]

← Older revision	Revision as of 02:00, 28 March 2014
(No difference)

@@ Line 34: / Line 34: @@
 # fetch the secondary structure assignment from the PDB &
 # split it up into an array of characters
-stored.ss = [ x for x in server.getKabschSander("1foo", "A") ]
+stored.ss = list( server.getKabschSander("1foo", "A") )
 # get the sequence

PDB Web Services Script - Revision history

Pyadmin: 6 revisions

Newacct: /* The Code */

Newacct at 10:22, 26 January 2010