Hi JD, Many (all?) options are available from the Chimera command "findclash" itself, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> for example "log true" to send information to the Reply Log or "saveFile pathname" to write it to a text file with location/name pathname. Is that what you needed, or does the information need to be stored in an array or variable? 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 Oct 28, 2008, at 7:15 AM, Jean Didier Pie Marechal wrote:
Hi everyone, I am writing a script for which I need the number of clashes for a given selection for continuing.
My first thought was to simply run in my script: runCommand("findclash selection ignoreIntraRes false") after having selected the region I was interested in. However, I realize that I come to the recurrent problem: having the information I am interested in printed in the reply log. I don't know how to have the info passed into an array or any kind of variable in the python environment. Could you tell me how to do so please?
On the other side, I would be pleased if you could tell me what is the correct arguments I have to pass and syntax I have to use for the functions detectClash and/or cmdDetectClash (which I guess is the basis of the same findclash).
All the best, JD