[Chimera-users] writing a trajectory to multiple pdbs

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 16 13:13:20 PST 2010

Hi Dan,
You're right, currently the "save PDB" dialog and "write" commands,  
although they do have trajectory-specific options, can only save all  
the loaded frames into a single file.

The workaround is to first write the loaded frames of the trajectory  
as a single, multi-MODEL file, then read that file back in as a  
regular PDB file (instead of as a trajectory).  Then the frames will  
be loaded as multiple models and you can avail yourself of the multi- 
model option in the "save PDB" dialog for saving multiple files.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 16, 2010, at 12:44 PM, Dan Gurnon wrote:

> Hi everyone,
> How would one write a trajectory read into MD Movie to a series of  
> pdb files instead of one large file? I don't see a suitable option  
> specified for the "write" command, and for "Save PDB" it seems the  
> option of multiple files is only available when multiple models are  
> selected.
> Dan

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