VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Oct 31 2022 - 07:24:55 CDT

Hi Charles,

You could use the Colvars Dashboard and a spinAngle coordinate:
[ https://urldefense.com/v3/__http://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html*sec:cvc_spinAngle__;Iw!!DZ3fjg!9crlQ6LqvmtobC3RQi9CxI_TdqiFnK-ARNX6B0xD0dGQROkZS-DoTNKXHxNyAs0-v5NIz8bYAag86IWAJ9NdY2-u$ | https://urldefense.com/v3/__http://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html*sec:cvc_spinAngle__;Iw!!DZ3fjg!9crlQ6LqvmtobC3RQi9CxI_TdqiFnK-ARNX6B0xD0dGQROkZS-DoTNKXHxNyAs0-v5NIz8bYAag86IWAJ9NdY2-u$ ]

By default this will compute rotation around the z axis. You could align the protein in VMD first, or make the definition local to the protein frame of reference by defining a set of protein atoms as a fittingGroup .
https://urldefense.com/v3/__http://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html*sec:colvar_atom_groups_ref_frame__;Iw!!DZ3fjg!9crlQ6LqvmtobC3RQi9CxI_TdqiFnK-ARNX6B0xD0dGQROkZS-DoTNKXHxNyAs0-v5NIz8bYAag86IWAJynhZCsf$

Best,
Jérôme

----- Le 28 Oct 22, à 3:55, CPMAS Chen <cpmasmit_at_gmail.com> a écrit :

> Dear All,
> How to get the orientation angle of a helix relative to the protein's principal
> axis? For example the theta and phi angle of a helical region relative to the
> symmetrical axis of a pentameric protein?
> Theta can be obtained with fit_angle.tcl. How about phi, the rotation angle in
> the plane perpendicular to the principal axis?

> Thanks!

> Charles

> --

> ***************************************************

> Charles Chen

> Research Instructor

> University of Pittsburgh School of Medicine

> Department of Anesthesiology

> ******************************************************