[Chimera-users] PDB file format for movie

[Mingfeng Yang]

Thanks, Elaine and Eric. That works.

Mingfeng

On 2/5/07, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> 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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