[Chimera-users] suggestion for superimposig

[Elaine Meng]

On Aug 1, 2008, at 7:35 AM, Srinath Thiruneelakantan wrote:

> Hi,
> I am microbiologist and wanted to know the strucutre of a protein  
> of M. tuberculosis, whose crystal structure has not been solved,  
> but its homologue in Bacillus has been. So by Swiss-modeller  
> generated a MODEL and downloaded it in PDB format. Now I wanted to  
> superimpose the generated model with of bacillus and with PDB of  
> truncated protein of E. coli. As I am not of bioinformatic  
> bakground, please suggest me how to get the FINAL output in PDB  
> format so can have a comarison of domains between these three  
> proteins.
> Thank you,
> Srinath


Hi Srinath,
Just open all of the PDB files in Chimera (for example, with File...  
Open).  You can change the display if you want, for example with  
Presets... Interactive 1 (ribbons).

Then you can use the MatchMaker tool (under Tools... Structure  
Comparison) to superimpose the proteins.  Choose the "reference"  
structure on the left and one or more structures to match onto it on  
the right.  It usually does not matter which one you use as the  
"reference" - try using the first one listed.  In most cases, the  
default settings work well, so it is very easy: turn off "Show  
alignment(s)..." if you don't want to see the sequence alignments,  
but otherwise just click "Apply" to match the structures.  It will  
take a few seconds to compute the alignments and then match the  
structures. Then you can compare the structures in Chimera, or write  
out PDB as mentioned below.

If that does not give a good enough superposition, then you can try  
changing parameters.  For details see the MatchMaker manual page  
(simply clicking "Help" on the dialog will open your local copy):
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ 
matchmaker.html

These tutorials have examples of superimposing and comparing structures:
"Superpositions and Alignments"
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
alignments.html
"Structure Analysis and Comparison"
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html

Additional discussions about superimposing structures:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/ 
morph.html#superimposing
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
images.html#matching

After the proteins are superimposed, you can write out the structures  
as one or more PDB files with "File...  Save PDB" in the Chimera menu.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb

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