[Chimera-users] to view nmr pdb structures

[Elaine Meng]

On Jun 14, 2007, at 10:15 PM, Shunsuke Meshitsuka wrote:
> I have used chimera as a viewer of proteins.
> I have a question how to overlay the 20 structures of NMR pdb data by
> chimera.
> When there are 20 structures of structurename01.pdb,
> structurename02.pdb,,,structurename20.pdb, chimera structurename**.pdb
> makes a random location and random orientation of each protein.
> Please let me know the method.

Hi Shunsuke,
First I should mention there are two ways to read in the data:

(1) with all the different structures in one PDB file separated by  
MODEL and ENDMDL records, like the NMR structures in the PDB.  If  
opened as model 0 in Chimera, the structures can be specified as #0.1,  
#0.2, #0.3 ...

(2) with each structure a separate PDB file, as you described.  The  
structures can be specified as #0, #1, #2 ...

Then, there are many possible ways to match the structures in Chimera:

(A) use the "match" command and tell it which atoms to fit
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
...also covered in "Images" tutorial (go to the Matching Structures  
part)
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
frameimages.html

(B) use MatchMaker (under Tools... Structure Comparison), which makes a  
sequence alignment and then fits the CA atom pairs of the aligned  
residues
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/ 
matchmaker.html
...also covered in "Alignments" tutorial
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
alignments.html

(C) use the "matchmaker" command, which works the same way as MatchMaker
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html

(D) use EnsembleMatch (under Tools... Structure Comparison) - only  
works when the structures are together in one PDB file
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblematch/ 
ensemblematch.html
...also covered near the end of the "Ensembles and Model Panel" tutorial
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
ensembletut.html

See also these recent messages to chimera-users:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001566.html
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-June/001609.html

That should get you started!
Best,
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