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       g_helixorient  -  calculates  local  pitch/bending/rotation/orientation
       inside helices

       VERSION 4.0.1


       g_helixorient  -s   topol.tpr   -f   traj.xtc   -n   index.ndx   -oaxis
       helixaxis.dat  -ocenter  center.dat -orise rise.xvg -oradius radius.xvg
       -otwist  twist.xvg  -obending   bending.xvg   -otilt   tilt.xvg   -orot
       rotation.xvg  -[no]h  -nice  int  -b  time  -e  time -dt time -[no]xvgr
       -[no]sidechain -[no]incremental


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

       As input, you need to specify an index group with  alpha  carbon  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/CA-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 theta1-3.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


        Print help 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)

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

        Calculate sidechain directions relative to helix axis too.

        Calculate incremental rather than total rotation/tilt.



       More      information     about     GROMACS     is     available     at

                                Thu 16 Oct 2008               g_helixorient(1)