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
========================================
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