[Chimera-users] to view nmr pdb structures
meng at cgl.ucsf.edu
Fri Jun 15 09:49:23 PDT 2007
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
> 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.
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
...also covered in "Images" tutorial (go to the Matching Structures
(B) use MatchMaker (under Tools... Structure Comparison), which makes a
sequence alignment and then fits the CA atom pairs of the aligned
...also covered in "Alignments" tutorial
(C) use the "matchmaker" command, which works the same way as MatchMaker
(D) use EnsembleMatch (under Tools... Structure Comparison) - only
works when the structures are together in one PDB file
...also covered near the end of the "Ensembles and Model Panel" tutorial
See also these recent messages to chimera-users:
That should get you started!
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
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