[gmx-users] Definition of helicity

cd231 at ipc.uni-karlsruhe.de cd231 at ipc.uni-karlsruhe.de
Wed Mar 9 14:58:18 CET 2011

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?


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
> 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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