[Chimera-users] Multiple stucture comparision

[Elaine Meng]

Dear Pankaj,
All the methods in Chimera are pairwise, but you can still get a  
multiple superposition by doing multiple pairwise superpositions.  In  
fact, you can get a multiple superposition in one step using the  
MatchMaker tool - just choose one structure as the reference and  
multiple others as the structures to match.  Here is the manual page:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ 
matchmaker.html

There is also a "matchmaker" command that works the same way, and a  
"match" command in which you can specify exactly which atoms should  
be used; with those, you would need to use the command multiple times  
(once for each pairwise match).
Here are the manual pages for the commands:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html

The "Images for Publication" tutorial includes an example of  
superimposing 3 structures with either command (go to the "Matching  
Structures" section):
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
frameimages.html

I am not sure what you meant about being unable to perform multiple  
superposition, so I just listed the ways and where to look for more  
information.  If you still have problems after using this  
information, it might be an issue with your structures - if so, you  
could let us know what the structures are and more details about what  
you did and what happened in Chimera.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On May 19, 2007, at 6:23 AM, Pankaj Barah wrote:

> Dear all,
> I have been using UCSF Chimera for structural superpositions for  
> last few days. But while trying to do multiple superimposition for  
> a set of proteins, i am unable to perform it. can anybody give me  
> any suggestion?
> Regards
>
> Pankaj Barah
> Junior Research Fellow,   Phone:+91-9922346120(M)
> Bioinformatics Centre,         +91-20-25692039(O)
> University of Pune,
> Pune 411 007,Maharashtra, India.