[gmx-users] what is theta in g_helixorient?

Justin Lemkul jalemkul at vt.edu
Tue Oct 2 17:38:51 CEST 2012

On 10/2/12 11:35 AM, Albert wrote:
> On 10/02/2012 05:16 PM, Justin Lemkul wrote:
>> On 10/2/12 11:13 AM, Albert wrote:
>>> hello guys:
>>>    I am using g_helixorient to analyze the helix property in my system and it
>>> generate three theta[1,2,3].xvg  file. I am wondering what's that? I didn't find
>>> any comments in the help file.
>> Have you read the last paragraph of g_helixorient -h?
>> -Justin
> of course, here it is. I don't find anything related to my questions.
> Option     Filename  Type         Description
> ------------------------------------------------------------
>    -s      topol.tpr  Input        Run input file: tpr tpb tpa
>    -f       traj.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
>    -n      index.ndx  Input, Opt.  Index file
> -oaxis  helixaxis.dat  Output       Generic data file
> -ocenter center.dat  Output       Generic data file
> -orise     rise.xvg  Output       xvgr/xmgr file
> -oradius radius.xvg  Output       xvgr/xmgr file
> -otwist   twist.xvg  Output       xvgr/xmgr file
> -obending    bending.xvg  Output       xvgr/xmgr file
> -otilt     tilt.xvg  Output       xvgr/xmgr file
> -orot  rotation.xvg  Output       xvgr/xmgr file
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   yes     Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    19      Set the nicelevel
> -b           time   0       First frame (ps) to read from trajectory
> -e           time   0       Last frame (ps) to read from trajectory
> -dt          time   0       Only use frame when t MOD dt = first time (ps)
> -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -[no]sidechain bool no      Calculate sidechain directions relative to helix
>                              axis too.
> -[no]incremental bool   no      Calculate incremental rather than total
>                              rotation/tilt.

This is not the content to which I was referring.  There are input/output 
options.  The last paragraph of the help description is as follows:

"The tilt/rotation is calculated from Euler rotations, where we define the
helix axis as the local x-axis, the residues/Calpha vector as y, and the
z-axis from their cross product. We use the Euler Y-Z-X rotation, meaning we
first tilt the helix axis (1) around and (2) orthogonal to the residues
vector, and finally apply the (3) rotation around it. For debugging or other
purposes, we also write out the actual Euler rotation angles as theta[1-3].xvg"

I believe this answers your question.  Some help descriptions are quite long and 
the information you need may pass by in the terminal.  Everything contained in 
the help description for all tools is also printed in the manual.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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