[Chimera-users] Writing residues coordinates and COMs

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 14 09:42:07 PDT 2020

 Hi Yasser,
In general you should first figure out all the commands you need to use before putting them into python form.  (And then if there are some things not available as commands, they may be possible to do in python, but that is not the issue here.)

You can use a command to select the residue and then use the "write" command option "selected" to include only the atoms that are selected, for example, commands:

select #0:25.A
write selected 25.pdb


However, it will require more python knowledge to loop through all the residues and substitute their numbers into the "select" command (and output file name, if that's what you want).  I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 14, 2020, at 1:26 AM, Yasser Almeida <yasser.almeida at gmail.com> wrote:
> Hello,
> I am writing a python script to iterate through all the residues of my model and write the residue coordinates and its correspondent center of mass. I tried with 'runCommand' with the command 'write' but it only accepts a model to be written, not a specific residue.
> Any thoughts?
> Thanks in advance.
> Yasser

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