VMD-L Mailing List

From: Balazs Jojart (jojartb_at_pharm.u-szeged.hu)
Date: Tue Mar 31 2009 - 14:28:40 CDT

Hi folks,
I used the trajelix module of SIMULAID packge developed by Mihaly Mezei,
and it is very useful.
(http://atlas.physbio.mssm.edu/~mezei/simulaid/)
The program is able to calculate helix displacments, rotation, tilt
angles etc.
hope this helps,
Balazs

Peter Freddolino wrote:
> 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.
>>>>>>>
>>
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