RASTEP(1)RASTEP(1)NAMErastep - (Raster3D Thermal Ellipsoid Program)
SYNOPSISrastep [-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 sta‐
tistical 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 enclos‐
ing an isosurface of the probability density function. These are com‐
monly 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
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 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
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 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 ALSOraster3d(l), render(l)AUTHORS
Ethan A Merritt.
Raster3D 14 Dec 2010 RASTEP(1)
