[Chimera-users] Multiple stucture comparision

Elaine Meng meng at cgl.ucsf.edu
Sat May 19 12:40:53 PDT 2007

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:

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:

The "Images for Publication" tutorial includes an example of  
superimposing 3 structures with either command (go to the "Matching  
Structures" section):

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 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

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.

More information about the Chimera-users mailing list