Hi Samo, Strictly speaking, the answer is no. However, you can call the Python function that Surfnet uses with some simple Python code, namely: from Surfnet import interface_surfnet Interface_surfnet("#0", "#0") This assumes you want to run Surfnet on all of model #0. You can use different atom specs in the second line above if you want to do something different than that. Anyway, you can put those two lines in the MD Movie's Per Frame→define script dialog ("Interpret script as Python" in the resulting dialog), or put them in a file ending with .py and open that .py file every trajectory frame (again, probably with the "define script" dialog). --Eric Eric Pettersen UCSF Computer Graphics Lab

On Aug 31, 2022, at 12:49 AM, Samo Lešnik via Chimera-dev <chimera-dev@cgl.ucsf.edu> wrote:

Dear Madam/Sir,

I was wondering if it is possible to run the Surfnet calculation using the command line tool. I wish to automate it for MD trajectory for every frame and this would be useful.

Thank you!

Samo

Dr. Samo Lešnik, mag. farm. / Researcher Univerza v Mariboru / University of Maribor Fakulteta za kemijo in kemijsko tehnolgijo Faculty of Chemistry and Chemical Engineering Smetanova ulica 17, 2000 Maribor, Slovenija T: +386 2 2294 428 E: samo.lesnik@um.si <mailto:samo.lesnik@um.si> _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev>