Hi Yogesh - You may be able to do something similar to the antibody elbow angle script on the PyMOL Wiki (and PyMOL-scripts GitHub repo) using rotation matrices aligning various subunits to determine the principal axis. Or if you already have a way of calculating the principal axis, you can use Christoph Gohlke’s transformations.py module (which is used by the elbow angle script) to calculate the angle.
I’m away from my computer at the moment but those two scripts should be fairly easily found using your favorite search engine. Hope that helps. Cheers, Jared On Tue, Nov 9, 2021 at 8:03 AM Yogesh Sharma <yogesh.rm...@gmail.com> wrote: > Hi I want to get angle between a molecules principal axis and systems z > axis iteratively over 100ns trajectory. I am new to pymol. Can someone help > me with scripting it out? Thank you for your time. > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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