Tara,
Use Python (and the run command with .py files).
from pymol import cmd
f=open('dist.txt','w')
dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha')
f.write(%8.3f\n%dst)
f.close()
You could measure the whole protein this way by putting a loop around the
distance command:
from pymol import cmd
f=open('dist.txt','w')
atom = cmd.get_model(mol1ha).atom
for i in range(len(atom)-1):
sele1 = 'mol1///%s/HA'%atom[i].resi
sele2 = 'mol1///%s/HA'%atom[i+1].resi
dst=cmd.distance('tmp',sele1,sele2)
f.write(%14s %14s %8.3f\n%(sele1,sele2,dst))
f.close()
The output dist.txt would then look like:
mol1///4/HAmol1///5/HA4.748
mol1///5/HAmol1///6/HA4.828
mol1///6/HAmol1///7/HA4.861
mol1///7/HAmol1///8/HA4.784
mol1///8/HAmol1///9/HA4.936
mol1///9/HA mol1///10/HA4.833
mol1///10/HA mol1///11/HA4.933
mol1///11/HA mol1///12/HA4.813
etc.
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
-Original Message-
From: Tara Sprules [mailto:tspru...@ualberta.ca]
Sent: Wednesday, January 08, 2003 3:20 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] measuring distances
Hi,
I have a file which measures a bunch of distances between
atoms (of the
form distance (mol1///25/ha), (mol1///26/ha)), and rather
than having to
look at the results on the screen I'd like to have the values output
to a text file. Is it possible to do this?
Thanks,
Tara
Tara Sprules
Post-Doctoral Fellow
Department of Chemistry
University of Alberta
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