VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 31 2009 - 12:16:57 CDT

Nifty... thanks!
Peter

Thomas C. Bishop wrote:
> I had less than a two turns to play with and it was clear that was not
> enough... more is better I know that :-)
>
> Cesar Millan seems to have found the answer...
> The proper solution appears to be available in charmm
>
> the coor helix command does it.
>
> here's an "unofficial" link to what coor helix does.
>
> http://icbtools.med.cornell.edu/prokink/charmm_helix.html
>
>
>
> Tom
>
>
> On Tuesday 31 March 2009, Peter Freddolino wrote:
>> 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.
>
>
>