Hi Sebastian, the second link below shows how to put Chimera commands in python scripts:
See these previous posts for more general information on scripts: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003261.html
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003262.html
Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Nov 18, 2008, at 2:23 AM, Sebastian Kruggel wrote:
Hi Elaine,
thanks for the ideas - indeed it seems to be the simplest way to write a small python script to loop over the ligands and use the rmsd command (indeed I'm interested in the RMSD values as they are and no best-fit). The examples I found in the mailing list were command scripts - if I use python (to get better possibilities to loop etc), how do I combine for instance the rmsd command in the script?
for i in os.system('./'): rmsd #1.1 #1.i
gives syntax error - of course because of the python/chimera mixture... But how can I combine these two correctly? Sorry for these basic quesions...
Best regards Sebastian
Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 D 20146 Hamburg Tel +49(0) 40 42838 3626