[Chimera-users] matchmaker

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 6 09:21:39 PST 2010

Hi Damien,
You can tell Matchmaker which chains to use.  In 1ofu, the copies of  
Ftsz are chains A and B.

In the Matchmaker GUI, there is a "chain pairing" section where "Best- 
aligning pair..." is the default.  You could change that to the  
"Specific chain(s) in reference structure with specific chain(s) in  
match structure" and then from the top section choose the chains to  
use.  In your example, you would pick one copy of 1fsz (which only has  
chain A) to pair with chain A of 1ofu.  Then in the second match, you  
would pick the other copy of 1fsz chain A to pair with chain B of  
1ofu.  Click the "Help" button on the MatchMaker dialog to see the  
full documentation, or view it at our site:

You can also do it with the command version of matchmaker using the  
"pair ss" option, for example:

mm #0:.a #1:.a pair ss

Full description of the many matchmaker command options:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 6, 2010, at 6:18 AM, Damien Larivière wrote:

> Dear all,
> I opened the pdb 1OFU (SulA-FtsZ complex) and visually I am not sure  
> where is exactly the protein FtsZ in this complex and also whether  
> FtsZ is complete or not.
> So I opened the pdb 1FSZ which is one structure for FtsZ and I  
> applied Matchmaker. The result is the superimposition of this  
> protein with the complex.
> However, the complex is made of two FtsZ proteins, each at one end  
> of the complex. So I opened again the pdb 1FSZ and applied  
> Matchmaker in order to get each end superimposed with one FtsZ  
> protein. But what I obtained is the same result obtained during the  
> first use of Matchmaker: both FtsZ are superimposed at the same  
> place. May you tell me how to specify the software not to use the  
> same location?
> I join the Chimera session. Many thanks for your help.
> Damien

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