VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_tulane.edu)
Date: Tue Mar 31 2009 - 10:08:51 CDT

Such an approach is really susceptible to exactly the problem I described.
If you chose residues i thru i + N as the helix and calc the principal axes
you'll find that as you change N the axis of the helix gradually precesses
about what you "know" is the proper axis. each additional residue biases the
direction axis direction toward itself. Unless you have several turns the
bias is rather strong.

The proper method would be to actually fit the mathematical expression for a
helix to the Ca atoms of the alpha helix. I don't think this will have the
same biasing problem

Tom

On Tuesday 31 March 2009, Peter Freddolino wrote:
> 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. 

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