Hi Thu,
If you know the correct Chimera command, then you could just use runCommand in python, as explained in this page:
http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html
I don't know python, but as for the Chimera "distance" command, it requires exactly two atoms (not two sets of atoms), e.g.
distance :628.a@ca :20.b@ca
However, in our list of python scripts for Chimera, I see there is already a script to find the minimum distance between two sets of atoms! You can get this script "atomdist.py" from:
http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Mar 24, 2015, at 6:20 AM, Hoai Thu NGUYEN
Hi, I need to calculate the minimum distance between 2 residues but It seems that I can't find the correct way to use the 'measure distance' command in python script. I tried:
import Measure
temp = Measure.measure_command('distance', 'distance :628.a :20.b')
but it gave me the error: "No target atoms or surface"
Can you please precise the correct syntax of this command? Thank you! Thu