[gmx-users] Definition of helicity

[Justin A. Lemkul]

cd231 at ipc.uni-karlsruhe.de wrote:
> Hi Justin,
> 
> Thank you for your notice.
> I am afraid my explanation was not enough.
> When protein atoms is specified, g_helix seems to calculate the 
> helicities for all residue.
> And then, the helicity value of each residues is written into helicity.xvg.
> The value probably means how much percentage of time does each residue 
> form alpha-helix.
> I would like to know how does it judge the alpha-helix? What is the 
> criterion?
> 

That is too broad of a question to get a useful answer.  Only you know your
intents.  What is it that you're looking to evaluate?  I don't know how one
generically judges an alpha helix aside from its basic geometry.  You'll have to
explain your goals very precisely if you want any more useful help.

-Justin

> Hiroshi
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>>
>>
>> cd231 at ipc.uni-karlsruhe.de wrote:
>>> Dear all,
>>>
>>> Now I am using g_helix module to calculate helicity of each residues in
>>> protein.
>>> In the manual, there seems to be no detailed description about the
>>> definition of the helicity.
>>> Could you let me know the detail, or where should I refer to.
>>>
>>
>> As implied by the rise and ellipticity information in the g_helix 
>> description,
>> it would seem that an ideal helix is an alpha helix.  I doubt this 
>> tool is
>> useful when analyzing single residues; the program determines the longest
>> continuous alpha helix and calculates properties related to it.  
>> g_helix may
>> work on a single residue, but if you get output of all zeroes, don't be
>> surprised.  do_dssp may also be useful.
>>
>> -Justin
>>
>>> Thank you in advance,
>>>
>>> Hiroshi
>>> ----------------------------------------
>>> Hiroshi Watanabe
>>> Karlsruhe University
>>> E-mail: hiroshi.watanabe at chemie.uni-karlsruhe.de
>>>
>>>
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================