VMD-L Mailing List

From: Goutham (gouthambs_at_gmail.com)
Date: Tue Mar 31 2009 - 10:30:30 CDT

I once had to do something very similar. If you know the range of
atoms/residues that form an alpha helix, then you can find the principal
axes of the helical part to define the axis. I used the linear algebra
package to find the principal axis etc. :

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

THe orient package has the commands to find principal axis. If you use the
above package, the I_3 (third component of principal axes) is what you are
looking for...

Best
Goutham

On Tue, Mar 31, 2009 at 7:44 AM, Thomas C. Bishop <bishop_at_tulane.edu> 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.
>
>
>
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