[Chimera-users] Converting a part of a molecule in pdb to xyz format

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 22 10:41:17 PST 2017


Hi Vladyslav,
In Chimera you can select part of the structure and then save only the selected atoms (it is an option in the File… Save PDB dialog), but it will stil be PDB format.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

Chimera does not convert PDB to XYZ  format, so you would need to find some other program to do that part -- maybe openbabel?
Best,
Elaine
-----
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 22, 2017, at 12:00 AM, Vladyslav Dziuba <xenonbat at ya.ru> wrote:
> 
> Greetings.
> Could you possibly help me with cobverting of pdb to xyz? I need to select a part of a molecule, "cut it out", and write coordinates of this part into xyz file. Is it possible? How to do that?
> 
> Thank you for your reply in advance
> 
> Best regards,
> Vladyslav Dziubz




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