[gmx-users] Definition of helicity

[Mark Abraham]

On 10/03/2011 12:58 AM, 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?

If g_helix -h doesn't help you, then you'll have to read the code for
the details of what criterion it is using. Presumably src/tools/gmx_helix.c

Mark

>
> 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
>>
>> ========================================
>> -- 
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>