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, omitting 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
merritt@u.washington.edu

SEE ALSO¶

raster3d(l), render(l)

AUTHORS¶

Ethan A Merritt.