[Chimera-users] PDB Header via command line?

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 20 09:28:12 PST 2014

Hi Korbin,
I don't know if this meets your needs, but:

In Chimera, the attached python script findIncomplete.py selects templated residues (e.g. standard amino acids) that are missing any nonhydrogen atoms.   It can only select atoms that are actually present, so it won't directly identify which atoms are missing.  You could write a list of the selection (e.g. command "writesel") but you would need to infer which atoms were missing from that list.  Also, this script wouldn't report residues that are completely missing.

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

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On Nov 20, 2014, at 7:25 AM, Korbin West <khwest16 at wabash.edu> wrote:

> Hi,
> I'm trying to find missing atoms in certain residues. I know they are in the pdb header information, but is there a way I can use Chimera or python script to access this using the command line only? I have a large number of proteins to go through, so checking them all individually is not really efficient.
> Korbin West

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