Hi Ryan, There are now Chimera commands "matchmaker" and "findclash" with many keyword options. The matchmaker command has all the same options as the GUI, while the findclash command has all the same options as the GUI except continuous monitoring. Man pages for those commands: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mmaker.html

<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/findclash.html

If you wanted outputs other than what the MatchMaker and Find Clashes GUIs and commands already provide, however (e.g. saving the sequence alignment from matchmaker to a file), python scripting may be required. You might be interested in these previous posts to the chimera-users list in which Eric provided scripts to write out additional information: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-December/002090.html

(initial script StructAlign2.py attached below) <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-December/002091.html

<http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-December/002092.html

(another script that does more stuff structAlign3.py attached below) In general, however, I recommend looking in the current documentation before the archive, which includes some out-of-date information. You can do a keyword search using "Help... Search Documentation" in the menu. That searches your local copy of the documentation included with the download, so will be as current as your download. Online, you can view the documentation of the latest production release here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/index.html I hope this helps, 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 Aug 11, 2008, at 9:32 AM, Ryan wrote:

Hi. I read in the archive (2004) that someone was looking to use MatchMaker in the nogui mode / command line, but that was not a possibility at the time. I am wondering if this ability has ever been implemented, and if so, how does one go about scripting this. Additionally, i would like to use the 'Find Clashes/Contacts' function in nogui mode. Is this possible? Thanks a lot,

ryan