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PROGRAM:
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]] < infile.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 statistical analysis of the atomic anisotropy for various
classes of input atoms. By default the program creates an ellipsoid+stick scene
description 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 -tabulate option, in which
the primary output to stdout is a list of the Eigenvalues of the Uij matrix, followed by
the corresponding atomic anisotropy 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 default 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 components
rastep -h -Bcolor 10. 30. < infile.pdb > ellipsoids.r3d
cat header.r3d ellipsoids.r3d otherstuff.r3d | render > picture.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 surface
-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 describe 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 ellipsoids. 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 instead. 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 fraction; 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 statistical 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 programs 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 contact:
Ethan A Merritt
University of Washington, Seattle WA 98195
[email protected]
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