# gmx-helixorient - Online in the Cloud

This is the command gmx-helixorient that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

### PROGRAM:

#### NAME

gmx-helixorient - Calculate local pitch/bending/rotation/orientation inside helices

#### SYNOPSIS

gmx helixorient [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
[-oaxis [<.dat>]] [-ocenter [<.dat>]] [-orise [<.xvg>]]
[-obending [<.xvg>]] [-otilt [<.xvg>]] [-orot [<.xvg>]]
[-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
[-[no]sidechain] [-[no]incremental]

#### DESCRIPTION

gmx helixorient 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.

Note 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 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

#### OPTIONS

Options to specify input files:

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:

-oaxis [<.dat>] (helixaxis.dat)
Generic data file

-ocenter [<.dat>] (center.dat)
Generic data file

-orise [<.xvg>] (rise.xvg)
xvgr/xmgr file

xvgr/xmgr file

-otwist [<.xvg>] (twist.xvg)
xvgr/xmgr file

-obending [<.xvg>] (bending.xvg)
xvgr/xmgr file

-otilt [<.xvg>] (tilt.xvg)
xvgr/xmgr file

-orot [<.xvg>] (rotation.xvg)
xvgr/xmgr file

Other options:

-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>
xvg plot formatting: xmgrace, xmgr, none

-[no]sidechain (no)
Calculate sidechain directions relative to helix axis too.

-[no]incremental (no)
Calculate incremental rather than total rotation/tilt.

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