VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 31 2009 - 09:51:11 CDT

One possibility would be to calculate the principal axes for each helix
(there's convenient code for this at
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/)
and then calculating the angle using the first principal axis of each helix.

Best,
Peter

Thomas C. Bishop wrote:
> Good question and I'd like to know the answer too.
> based on work some years ago (Bishop and Schulten 1995?)
> I know that unless you have several turns of the alpha helix fitting an axis
> to the helix is very much subject to where you defined the start and end fo
> the helix.
>
> Tom
> On Tuesday 31 March 2009, Alison Grinthal wrote:
>> This must be simple but I haven't yet found it (I'm still in the early
>> stages of trying to learn scripting): is there a way to determine the
>> central axis of an alpha helix, and to calculate the dihedral angle
>> between two such axes? If this is explained somewhere or there's a plugin,
>> please direct me. Thanks very much.
>
>
>