[Chimera-users] PDB file format for movie

[Elaine Meng]

Hi Mingfeng,
Each "snapshot" should start with a MODEL record and end with an  
ENDMDL (not END), see the description of "PDB, single file":

http://www.cgl.ucsf.edu/chimera/1.2304/docs/ContributedSoftware/movie/ 
framemovie.html

MD Movie will use the MODEL numbers as frame numbers, so they should  
start with 1 or 0 and increment by 1.

Most NMR structures in the PDB that include multiple models are done  
this way, so you could look at those as examples.  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




On Feb 5, 2007, at 8:08 AM, Mingfeng Yang wrote:

> Dear Chimera users and developers,
>
> I'd like to use chimera to view the motions of a protein. If all  
> the snapshots are to be saved in a single PDB file, what's the  
> correct format for them?
>
> I tried  the following, but chimera complained that a single  
> structure is included only.
>
> Thanks,
> Mingfeng
> ------------------
> MODEL 1
> ATOM      1  N   ALA     1      -4.564  -7.956  -6.531  1.00   
> 0.00           N
> ATOM      2  CA  ALA     1      -5.237  -8.746  -5.532  1.00   
> 0.00           C
> ATOM      3  C   ALA     1      -4.360  -9.172  -4.378  1.00   
> 0.00           C
> ...
> ATOM     81  HN  ALA    10       0.195  11.398   3.736  1.00   
> 0.00           H
> END
> MODEL 2
> ATOM      1  N   ALA     1      - 5.031  -8.234  -5.174  1.00   
> 0.00           N
> ....
> END
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