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g_helixorient(1) [debian man page]

g_helixorient(1)				 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				  g_helixorient(1)

NAME
g_helixorient - calculates local pitch/bending/rotation/orientation inside helices VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
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 -[no]version -nice int -b time -e time -dt time -xvg enum -[no]sidechain -[no]incremental DESCRIPTION
g_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 FILES
-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]hno Print help info and quit -[no]versionno 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]sidechainno Calculate sidechain directions relative to helix axis too. -[no]incrementalno Calculate incremental rather than total rotation/tilt. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_helixorient(1)

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g_bundle(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_bundle(1)

NAME
g_bundle - analyzes bundles of axes, e.g. helices VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_bundle -f traj.xtc -s topol.tpr -n index.ndx -ol bun_len.xvg -od bun_dist.xvg -oz bun_z.xvg -ot bun_tilt.xvg -otr bun_tiltr.xvg -otl bun_tiltl.xvg -ok bun_kink.xvg -okr bun_kinkr.xvg -okl bun_kinkl.xvg -oa axes.pdb -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -xvg enum -na int -[no]z DESCRIPTION
g_bundle analyzes bundles of axes. The axes can be for instance helix axes. The program reads two index groups and divides both of them in -na parts. The centers of mass of these parts define the tops and bottoms of the axes. Several quantities are written to file: the axis length, the distance and the z-shift of the axis mid-points with respect to the average center of all axes, the total tilt, the radial tilt and the lateral tilt with respect to the average axis. With options -ok, -okr and -okl the total, radial and lateral kinks of the axes are plotted. An extra index group of kink atoms is required, which is also divided into -na parts. The kink angle is defined as the angle between the kink-top and the bottom-kink vectors. With option -oa the top, mid (or kink when -ok is set) and bottom points of each axis are written to a .pdb file each frame. The residue numbers correspond to the axis numbers. When viewing this file with Rasmol, use the command line option -nmrpdb, and type set axis true to display the reference axis. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -ol bun_len.xvg Output xvgr/xmgr file -od bun_dist.xvg Output xvgr/xmgr file -oz bun_z.xvg Output xvgr/xmgr file -ot bun_tilt.xvg Output xvgr/xmgr file -otr bun_tiltr.xvg Output xvgr/xmgr file -otl bun_tiltl.xvg Output xvgr/xmgr file -ok bun_kink.xvg Output, Opt. xvgr/xmgr file -okr bun_kinkr.xvg Output, Opt. xvgr/xmgr file -okl bun_kinkl.xvg Output, Opt. xvgr/xmgr file -oa axes.pdb Output, Opt. Protein data bank file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno 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) -tu enum ps Time unit: fs, ps, ns, us, ms or s -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -na int 0 Number of axes -[no]zno Use the z-axis as reference instead of the average axis SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_bundle(1)
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