Maybe I'm understanding the question wrong, but here is a solution for
getting a list of all atom-atom distances between a ligand and a protein.
Just change the pdb id, and the definitions of the protein and ligand to
your case. A list of these distances will then be in the dist_list
object, which you can do anything you want with. In the example I
simply printed them out.
To run example below (if saved as distlist.py) from pymol:
run distlist.py
~ Dan
---
Dan Kulp
Biophysics Graduate Student @ UPenn
dwk...@mail.med.upenn.edu
http://dwkulp.homelinux.net/tiki/tiki-index.php
---
import cmd
cmd.load("1O2K.pdb")
cmd.select("protein","not resn 656 and not resn HOH")
cmd.select("ligand", "resn 656")
dist_list = {}
pro_atoms = cmd.get_model("protein")
lig_atoms = cmd.get_model("ligand")
for l_at in lig_atoms.atom:
for p_at in pro_atoms.atom:
dist_list[str(l_at.resi)+":"+l_at.name+";"+str(p_at.resi)+":"+p_at.name]
= cmd.dist("foo", "index "+str(l_at.index),"index "+str(p_at.index))
cmd.delete("foo")
print "LIST OF ATOM-ATOM PROTEIN-LIGAND DISTANCES"
for d in dist_list.keys():
print "Distance of "+d+" is "+str(dist_list[d])
--
Warren DeLano wrote:
Stephanie,
This is a very reasonable request, but unfortunately it is not one that
PyMOL can meet at present -- it will require some significant changes
within the C code for the "distance" command.
Thank you for the suggestion.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Stephanie Endsley
Sent: Wednesday, May 18, 2005 3:38 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] listing distance measurements
Hi there,
I can get MacPyMol to find distances between a ligand and
protein, but I want to output a list of all of these
distances. I have looked everywhere on how to do this, and I
saw another posting with the same question, but it wasn't answered.
Does anyone out there know how to get a list of the distances
that PyMol calculates? Please help.
Thanks
Steph
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