[Chimera-users] superimposed 3D structure

[Elaine Meng]

Hi Deeba,
Here is the User's Guide page about the different ways to superimpose  
structures in Chimera:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

It sounds like matchmaker would probably be the best way in your  
situation, and it can be used with  the graphical interface (in the  
menu, choose Tools... Structure Comparison... MatchMaker):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html 
 >
or the "matchmaker" command:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>

The exact command could depend on what models and chains you have, how  
similar they are, etc.  Please see the "matchmaker" manual page (link  
above) for details on the many options and some examples.  However,  
here is a very simple example command if your structures are models #0  
and #1 and you just want to use default settings:

mm #0 #1

Matchmaker is also used in various tutorials, for example:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html 
 >
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html 
 >

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


On May 8, 2010, at 1:01 AM, deeba noreen wrote:

> I am trying to make superimpose two similar proteins. To evalute its  
> structural differences regarding functional aspects, I want to  
> derive a superimposed model. I am using Chimera format... Can you  
> please tell me in terms of commands so i can apply.
>