[gmx-users] Definition of helicity

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 9 13:22:34 CET 2011

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.


> 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


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