Hi Samo, I believe it would make more sense to script Modeller directly since you have a local installation. Chimera doesn’t have commands for running Modeller. If you just script Modeller, you have access to all its options, not just the few that happen to show up in the Chimera interface. See the Modeller website and documentation there: <https://salilab.org/modeller/> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 10, 2019, at 9:36 AM, Samo Lešnik <samo.lesnik@gmail.com> wrote:

Dear Madam/Sir, I would like to run the Modeller missing loop function implemented in Chimera by using a Python script, as I want to go through a number of protein structures.

Is this possible? I do not find the appropriate commands in the comand list. I would use a local instalation of Modeller.

Thank you for your help. Best regards, Samo