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RASTEP(1)		    General Commands Manual		     RASTEP(1)

NAME
       rastep -	(Raster3D Thermal Ellipsoid Program)

SYNOPSIS
       rastep [-h] [-iso] [-Bcolor Bmin	Bmax] [-prob Plevel] [-fancy[0-3]]
       [-radius	R] < infile.pdb	> ellipsoids.r3d

       rastep -tabulate	[tabfile] [-by_atomtype] [-com [comtabfile]] < in-
       file.pdb	> statistics.text

       Rastep reads a PDB coordinate file.  This file must contain ANISOU
       records describing atoms	refined	anisotropically.  Rastep can either
       create an input file for	the Raster3D render program or perform a sta-
       tistical	analysis of the	atomic anisotropy for various classes of input
       atoms.  By default the program creates an ellipsoid+stick scene de-
       scription in which each atom  is	represented by an ellipsoid enclosing
       an isosurface of	the probability	density	function.  These are commonly
       known as	thermal	ellipsoids.

       The program can be run in an alternate mode, controlled by the -tabu-
       late option, in which the primary output	to stdout is a list of the Ei-
       genvalues of the	Uij matrix, followed by	the corresponding atomic an-
       isotropy	and isotropic Ueq, for each atom in the	input file with	both
       an ATOM record and a matching ANISOU record.  This mode is used by the
       validation tools	Parvati	and Skittls.

EXAMPLES
       To describe thermal ellipsoids at the 50% probability level, with de-
       fault CPK colors, and send it for immediate rendering into a PNG	file

	    rastep < infile.pdb	| render -png picture.png

       To describe the same ellipsoids colored by Biso,	omiting	header records
       so that the resulting input file	can be merged with other scene compo-
       nents

	    rastep -h -Bcolor 10. 30. <	infile.pdb > ellipsoids.r3d
	    cat	header.r3d ellipsoids.r3d otherstuff.r3d | render > pic-
       ture.png

OPTIONS
       -auto

       Auto-selection of viewing angle,	chosen to minimize the spread of the
       atoms along the view direction.

       -Bcolor Bmin Bmax

       Assign colors based on B	values rather than mathcing ATOM records
       against input or	default	COLOUR records.	Atoms with B <=	Bmin will be
       colored dark blue; atoms	with B >= Bmax will be colored light red;
       atoms with Bmin < B < Bmax will be assigned colors shading smoothly
       through the spectrum from blue to red.

       -fancy[0-6]

       The -fancy option selects increasingly complex representations of the
       rendered	ellipsoids.
	 -fancy0 [default] = solid surface
	 -fancy1 = principal axes of ellipsoid,	with transparent bounding sur-
       face
	 -fancy2 = colored equatorial planes of	the ellipsoid
	 -fancy3 = colored equatorial planes with transparent bounding surface
	 -fancy4 = transparent bounding	surface	containing longest principle
       axis
	 -fancy5 = for ORTEP lovers, a solid ellipsoid with one	octant missing
	 -fancy6 = for ORTEP lovers who	want the missing octant	in a separate
       color

       -h

       Suppress	header records in output.  By default rastep will produce an
       output file which starts	with header records containing a default set
       of scaling and processing options.  The -h flag will suppress these
       header records.	This option is useful for producing files which	de-
       scribe only part	of a scene, and	which are to be	later combined with
       descriptor files	produced by other programs.

       -iso

       Force isotropic probability surfaces (spheres). By default rastep will
       look for	ANISOU records in the PDB file and use these to	generate el-
       lipsoids.  If no	ANISOU record is present for a given atom, the B value
       given in	the ATOM/HETATM	record will be used to generate	a sphere in-
       stead. Selecting	the -iso option	will force the program to use the B
       value in	the ATOM record	even if	an ANISOU record is also present.

       -mini

       Auto-orientation	(as in -auto) and small	size plot (176x208).

       -nohydrogens

       Do not plot hydrogens, even if present in PDB file.

       -prob Plevel

       By default, isosurfaces are drawn to enclose the	50% probability	level
       in the density function described by the	Uij values in the ANISOU
       record.	The -prob option allows	you to select a	different probability
       level instead. If 0 < Plevel < 1	this value is interpreted as a frac-
       tion; if	Plevel > 1 this	value is interpreted as	a percent.

       -radius R

       By default, rastep draws	bonds with radius 0.10A	between	neighboring
       atoms using the same algorithm as rods. This option allows you to
       change the radius of the	bonds. If the radius is	set to 0 no bonds are
       drawn.

       -tabulate [tabfile]

       The -tabulate option requests that the program accumulate and print
       statistics on the distribution of anisotropy among atoms	in the input
       file rather than	producing an input file	for render. The	principle axes
       and anisotropy of each atom are written to stdout. An overall statisti-
       cal summary is written to tabfile if specified, otherwise to stdout.

       -by_atomtype

       The -by_atomtype	option is a modifier to	-tabulate. It causes a further
       subdivision of atoms by atom type in the	preparation of statistical
       summaries. Atom types are taken from columns 77:78 of the PDB ATOM
       records.

       -com [comtabfile]

       Tabulate	distribution of	anisotropy in shells by	distance from center-
       of-mass.	Output to comtabfile if	specified, otherwise to	stdout.

NOTES
       There is	little,	if any,	consistency in format among the	various	pro-
       grams which write out anisotropic displacement parameters. This program
       interprets the Uij values in the	order specified	for ANISOU records in
       PDB format.  That is, columns 29-70 of the PDB record are interpreted
       as integers representing	10000 *	Uij, in	the order U11 U22 U33 U12 U13
       U23.  Note in particular	that the order of the cross-terms is not the
       same as that used by ORTEP or shelx, neither of which use PDB format
       anyway.	However, the program shelxpro will produce correctly formatted
       PDB records from	a shelx	coordinate file.

SOURCE
       web URL:
	    http://www.bmsc.washington.edu/raster3d/raster3d.html con-
       tact:
	    Ethan A Merritt
	    University of Washington, Seattle WA 98195
	    merritt@u.washington.edu

SEE ALSO
       raster3d(l), render(l)

AUTHORS
	    Ethan A Merritt.

Raster3D			  14 Dec 2010			     RASTEP(1)

NAME | SYNOPSIS | EXAMPLES | OPTIONS | NOTES | SOURCE | SEE ALSO | AUTHORS

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