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("mol1////ha").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/HA mol1///5/HA 4.748
mol1///5/HA mol1///6/HA 4.828
mol1///6/HA mol1///7/HA 4.861
mol1///7/HA mol1///8/HA 4.784
mol1///8/HA mol1///9/HA 4.936
mol1///9/HA mol1///10/HA 4.833
mol1///10/HA mol1///11/HA 4.933
mol1///11/HA mol1///12/HA 4.813
etc.
Cheers,
Warren
--
mailto:[email protected]
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:[email protected]]
> Sent: Wednesday, January 08, 2003 3:20 PM
> To: [email protected]
> 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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