Thank you! --sv ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, August 13, 2009 2:05 PM To: Lockwood, Svetlana Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Scripting with Chimera Hi Svetlana, Every Chimera command can be pythonized with runCommand, as detailed in this previous post by Eric: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003729.html> We have reproduced the Ubuntu problem and are looking into it. Best, Elaine ----- Elaine C. Meng, Ph.D. 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 Aug 13, 2009, at 1:40 PM, Lockwood, Svetlana wrote:
Hi All,
Here's my problem: I need to calculate hydrogen bonds for several thousand PDB files. Chimera has nice hbonds command line command - sweet! Since Chimera was vanishing from Ubuntu, I had to switch to other available tools, i.e. Windows. After I got my python up and running and communicating with Chimera modules. Here's my very simple pseudo-idea:
foreach file in the list: open PDB file construct output filename from input filename calculate & and write out hydrogen bonds using hbonds command close file end foreach
Short and sweet. Except that one cannot use a command line command within python code. Command files don't work either because they do not understand python commands. Someone must have run into the same problem before me :-) Is there a way around this problem?
Thank you, Svetlana