VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 31 2009 - 10:18:06 CDT

Ah, I see... good point. It makes sense to fit a parametric expression
to the helix instead... the only problem I can think of with the fitting
approach is that it might have more trouble with helices that should
have curvature. Out of curiosity, how long, in your experience, does a
helix need to be before you start seeing convergence with the calculated
axis using, say, the principal axes?

Thanks,
Peter

Thomas C. Bishop wrote:
> 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.
>
>
>