[Chimera-users] Inter-helical angle?

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 23 10:49:07 PST 2011

Hi Brian,
You can use the Axes/Planes/Centroids tool to define helix axes, then get the angles between them.  It can do much more -- as implied by the name, you can define axes, planes, or centroids for various groups of atoms and then perform measurements among any of those objects.

- choose from menu: Tools... Structure Analysis... Axes/Planes/Centroids
- on the dialog, click "Define axes" and you might as well just take the defaults to define axes for all helices in your structure
- the axes will be listed in a table, and you can measure distances/angles between any pair by choosing them in the table (click on one, Ctrl-click on the second); that will report the crossing angle and distance at the bottom of the dialog and in the Chimera Reply Log

For more information on the tool and its options, see the manual page by clicking the Help button on the dialog, or going here:

You can also define axes and measure the angle with commands instead of the graphical interface:

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

On Feb 22, 2011, at 11:23 AM, Brian Cannon wrote:

> I need to calculate the angle between two helices in a protein.  Do you
> have any instruction about how I could go about doing this?
> Any help would be greatly appreciated.  Thanks!
> Brian

More information about the Chimera-users mailing list