[Chimera-users] PDB file format for movie

[Eric Pettersen]

Hi Mingfeng,
	Chimera's original PDB-parsing code was quite strict for exact  
format adherence.  Over time, I have made it more forgiving in many  
ways, but right now you're getting caught by one of it's remaining  
strictures:  according to the PDB format spec, the model number of a  
MODEL record has to be in columns 11-14.  In your example the model  
numbers start in column 7.  This problem will be fixed in the next  
snapshot, which we will be working on putting out next week.
	Also, as Elaine pointed out, you need to use ENDMDL records instead  
of END records.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu


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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