[Chimera-users] MatchMaker and Find Clash in nogui mode

[Elaine Meng]

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before the archive, which includes some out-of-date information.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 at 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

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