swift(8) [debian man page]

swift(8)						      System Manager's Manual							  swift(8)

NAME

       swift - Please fill

SYNOPSIS

       swift ...params...

DESCRIPTION

       swift

       Please fill in a long desc.

PARAMETERS

       param1

	      Describe here param1

																	  swift(8)

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

NAME

       do_dssp - assigns secondary structure and calculates solvent accessible surface area

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       do_dssp -f traj.xtc -s topol.tpr -n index.ndx -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa aver-
       area.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -sss string

DESCRIPTION

	do_dssp reads a trajectory file and computes the secondary structure for each time frame calling the dssp program. If you do not have  the
       dssp program, get it from http://swift.cmbi.ru.nl/gv/dssp.  do_dssp assumes that the dssp executable is located in  /usr/local/bin/dssp. If
       this is not the case, then you should set an environment variable  DSSP pointing to the dssp executable, e.g.:

	setenv DSSP /opt/dssp/bin/dssp

       The structure assignment for each residue and time is written to an  .xpm matrix file. This file can be visualized with for  instance	xv
       and  can  be  converted to postscript with  xpm2ps.  Individual chains are separated by light grey lines in the	.xpm and postscript files.
       The number of residues with each secondary structure type and the total secondary structure ( -sss) count as a function of  time  are  also
       written to file ( -sc).

       Solvent	accessible  surface  (SAS)  per residue can be calculated, both in absolute values (A2) and in fractions of the maximal accessible
       surface of a residue. The maximal accessible surface is defined as the accessible surface of a residue in a chain of glycines.	Note  that
       the program  g_sas can also compute SAS and that is more efficient.

       Finally,  this  program	can dump the secondary structure in a special file  ssdump.dat for usage in the program  g_chi. Together these two
       programs can be used to analyze dihedral properties as a function of secondary structure type.

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

       -ssdump ssdump.dat Output, Opt.
	Generic data file

       -map ss.map Input, Lib.
	File that maps matrix data to colors

       -o ss.xpm Output
	X PixMap compatible matrix file

       -sc scount.xvg Output
	xvgr/xmgr file

       -a area.xpm Output, Opt.
	X PixMap compatible matrix file

       -ta totarea.xvg Output, Opt.
	xvgr/xmgr file

       -aa averarea.xvg Output, Opt.
	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)

       -tu enum ps
	Time unit:  fs,  ps,  ns,  us,	ms or  s

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -sss string HEBT
	Secondary structures for structure count

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							do_dssp(1)