.TH g_helixorient 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_helixorient - calculates local pitch/bending/rotation/orientation inside helices

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_helixorient\fP
.BI "\-s" " topol.tpr "
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-oaxis" " helixaxis.dat "
.BI "\-ocenter" " center.dat "
.BI "\-orise" " rise.xvg "
.BI "\-oradius" " radius.xvg "
.BI "\-otwist" " twist.xvg "
.BI "\-obending" " bending.xvg "
.BI "\-otilt" " tilt.xvg "
.BI "\-orot" " rotation.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-xvg" " enum "
.BI "\-[no]sidechain" ""
.BI "\-[no]incremental" ""
.SH DESCRIPTION
\&\fB g_helixorient\fR calculates the coordinates and direction of the average
\&axis inside an alpha helix, and the direction/vectors of both the
\&Calpha and (optionally) a sidechain atom relative to the axis.


\&As input, you need to specify an index group with Calpha atoms
\&corresponding to an alpha\-helix of continuous residues. Sidechain
\&directions require a second index group of the same size, containing
\&the heavy atom in each residue that should represent the sidechain.


\&\fB Note\fR that this program does not do any fitting of structures.


\&We need four Calpha coordinates to define the local direction of the helix
\&axis.


\&The tilt/rotation is calculated from Euler rotations, where we define
\&the helix axis as the local \fI x\fR\-axis, the residues/Calpha vector as \fI y\fR, and the
\&\fI z\fR\-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 \fB theta[1\-3].xvg\fR
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-oaxis" " helixaxis.dat" 
.B Output
 Generic data file 

.BI "\-ocenter" " center.dat" 
.B Output
 Generic data file 

.BI "\-orise" " rise.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-oradius" " radius.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-otwist" " twist.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-obending" " bending.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-otilt" " tilt.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-orot" " rotation.xvg" 
.B Output
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]sidechain"  "no    "
 Calculate sidechain directions relative to helix axis too.

.BI "\-[no]incremental"  "no    "
 Calculate incremental rather than total rotation/tilt.

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.