[Chimera-users] Generating a PDB file

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 19 11:29:02 PDT 2013

Dear Nathalia,
We have been careful to make PDB files saved from Chimera follow the official PDB format description, so that other programs that read PDB should be able to read them without problems.   I assume you are using "File… Save PDB" from the Chimera menu, or the "write" command.

Can Chimera open the file?  If not, please just start Chimera and use menu "Help… Report a Bug" and attach the PDB file (the bugreport dialog allows attaching a file) so that we can take a look at it.

If Chimera can read it, I really can't say why Pymol or other programs wouldn't like the file.  Maybe some users that also use both Chimera and Pymol can send some comments on this issue.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 19, 2013, at 5:10 AM, Nathalia Varejão <varejaon at gmail.com> wrote:

> To whom it may concern,
> I'm using the chimera to visualize a protein ligand docking, but I want to save the best model as a PDB file that I can use anywhere to perform other analysis, is it possible? For example, the pdb that I saved by the chimera do not open in PyMol viewer...
> Can you help me?
> Nathalia

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