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/matchmak...
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.