text: ,
  Is there a way to incorporate dssp into pymol for secondary structure
  annotation?
  Thank you.
  SDA
  On Fri, Nov 28, 2008 at 1:39 PM, DimitryASuplatov <genesup@...> wrote:
  > Hello,
  > Is there a way to incorporate dssp into pymol for secondary structure
  > annotation?
  > Thank you.
  > SDA
  >
  >
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  -->> Message: 2
  >> Date: Fri, 28 Nov 2008 16:39:19 +0300
  >> From: DimitryASuplatov <genesup@...>
  >> Subject: [PyMOL] Secondary structure elements
  >> To: pymol-users@...
  >> Message-ID: <1227879559.914.24.camel@...>
  >> Content-Type: text/plain
  >>
  >> Hello,
  >> Is there a way to incorporate dssp into pymol for secondary structure
  >> annotation?
  >> Thank you.
  >> SDA
  [ ..snip .. ]
  >> Message: 3
  >> Date: Fri, 28 Nov 2008 14:15:57 +0000
  >> From: "gilleain torrance" <gilleain.torrance@...>
  >> Subject: Re: [PyMOL] Secondary structure elements
  >> To: pymol-users <pymol-users@...>
  >> Message-ID:
  >> <d0d153660811280615x514c775flb2316a24bf5935a4@...>
  >> Content-Type: text/plain; charset=ISO-8859-1
  >>
  >>
  SDA & Gilleain,
  I'm not sure this will help -- hopefully it'll help someone, but PDB + PyMOL =
  cool tricks. Here's a small script that will:
  (1) fetch a PDB
  (2) use the PDB web services to get the SS from PDB (KabschSander SS)
  (3) change the SS to match that from the PDB
  You can easily modify this to fetch and insert your own features.
  #
  # -- PDB Web Services Example
  # -- Posted on the PyMOLWiki:
  # --
  #
  import pymol
  from pymol import stored, cmd
  import SOAPpy
  import string
  # define a mapping from three letters to one
  # Thanks to whomever posted this on the PyMOLWiki:
  #
  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 = string.join( stored.pyMOLSeq, '' )
  server = SOAPpy.SOAPProxy("";)
  # 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")
  offset = string.find( pdbSeq, 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)" )
  cmd.as("cartoon")
  -- Jason
  --
  Jason Vertrees, PhD
  Dartmouth College : jv@...
  Boston University : jasonv@...
  PyMOLWiki :
  Jason Vertrees, PhD
  Boston U. -- jasonv@...
  Dartmouth -- jv@...
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