[Chimera-users] How to calculate the angle between two helix in a protein structure

[Elaine Meng]

> Date: Wednesday, March 30, 2016 9:20 AM
> Subject: How to calculate the angle between two helix in a protein structure
> 
> Dear community,
> 
> I want to calculate the angle between two helix in a protein structure. Does anybody know how to calculate it precisely?
> Please help me. Thanks a lot.
> 
> Best regards,
> Bing Wang
> National Institute of Biological Sciences, Beijing

Dear Bing Wang,

It can be done either with graphical interfaces (tool dialogs) or with commands.

You can calculate and display helix axes with the Axes/Planes/Centroids tool (in menu under Tools… Structure Analysis) or the “define” command.  The axes objects will be listed in in a dialog, and you can measure the angle between any two by choosing them in the dialog with the mouse, or by specifying their identifiers (as listed in the dialog) in the “angle” command.

See manual pages:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

Example commands (start Command Line from the Favorites menu):

open 2gbp
define axis perHelix true
angle a3 a10

This reports in the Reply Log (open from Favorites menu) that the angle between a3 and a10 is 22.893 degrees.  The dialog shows that I have axes a1-a10 calculated from the 10 helices in the structure 2gbp.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. Chimera questions should be sent to the chimera-users email address CC’d here… looks like you accidentally sent the question to just “chimera” instead