[gmx-users] what is theta in g_helixorient?

[Albert]

IC.

thanks a lot for kind comments.



On 10/02/2012 05:38 PM, Justin Lemkul wrote:
>
>
> 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
>
> -- 
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================