How to make script to run chimera command like add H and charged for multiple file
Dear Chimera Staff,
I want to run some chimera commands (such as add hydrogen and add charge) via python script for multiple files and save them as mol2 or pdb. I have read some examples, but still know nothing. Would you like to give me more about the script, how to make it easily?
Thank you
Best regards,
Hi Broto, I can't really say anthing more than is already in the written help:
First, figure out the Chimera commands that you need, such as by typing them into the command line.
Second, after you figure out the Chimera commands, then this page explains how to put them into a python script and run on multiple structure files. https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html
See the Programmer's Guide for more info and example scripts: https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2023, at 4:14 AM, Broto Santoso via Chimera-dev chimera-dev@cgl.ucsf.edu wrote:
Dear Chimera Staff,
I want to run some chimera commands (such as add hydrogen and add charge) via python script for multiple files and save them as mol2 or pdb. I have read some examples, but still know nothing. Would you like to give me more about the script, how to make it easily?
Thank you
Best regards,
-- Broto Santoso Laboratorium Kimia Farmasi Fakultas Farmasi UMS mobile: +6282136414379 (no call, sms only) My Youtube Channel
Thank you Elaine, your information really helped me a lot. Finally, I got the right url link for many Chimera Scripts: https://www.rbvi.ucsf.edu//trac/chimera/wiki/Scripts
And I have already found what I want in here: https://sourceforge.net/p/rdkit/mailman/message/36610151/
Thanks again,
Best regards,
Broto Santoso
On Mon, 16 Jan 2023 at 00:12, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Broto, I can't really say anthing more than is already in the written help:
First, figure out the Chimera commands that you need, such as by typing them into the command line.
Second, after you figure out the Chimera commands, then this page explains how to put them into a python script and run on multiple structure files. https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html
See the Programmer's Guide for more info and example scripts: https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2023, at 4:14 AM, Broto Santoso via Chimera-dev <
chimera-dev@cgl.ucsf.edu> wrote:
Dear Chimera Staff,
I want to run some chimera commands (such as add hydrogen and add
charge) via python script for multiple files and save them as mol2 or pdb. I have read some examples, but still know nothing. Would you like to give me more about the script, how to make it easily?
Thank you
Best regards,
-- Broto Santoso Laboratorium Kimia Farmasi Fakultas Farmasi UMS mobile: +6282136414379 (no call, sms only) My Youtube Channel
participants (2)
-
Broto Santoso -
Elaine Meng