Main Table of Contents

Wed 13 Nov 2013


g_helixorient calculates the coordinates and direction of the average axis inside an alpha helix, and the direction/vectors of both the Cα and (optionally) a sidechain atom relative to the axis.

As input, you need to specify an index group with Cα atoms corresponding to an α-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 Cα 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/Cα 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


-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

Other options

-[no]h bool no 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.