RASTEP - Raster3D thermal ellipsoid program

# RASTEP

# Raster3D Thermal Ellipsoid Program

#### SYNOPSIS

    rastep < 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 with Anisotropic Displacement Parameters Uij. 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

Describe thermal ellipsoids at the 50% probability level, with default CPK colors, and send it for immediate rendering into a TIFF image file. The angle of view is automatically adjusted to spread atoms out as much as possible in the XY plane of the image:

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

Describe the same ellipsoids colored by Biso, and create an input module with no header records for inclusion in a composite image:

    rastep -h -Bcolor 10. 30. < infile.pdb > ellipsoids.r3d
    cat header.r3d ellipsoids.r3d otherstuff.r3d | render -jpeg > picture.jpeg

List anisotropy of individual atoms to stdout and summarize the distribution of anisotropy to a separate file:

    rastep -tab summary.out < infile.pdb > anisotropy.out

#### 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 matching 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 (see figure)

-fancy0 [default] solid surface
-fancy1 draw principal axes of ellipsoid with a transparent bounding surface
-fancy2 draw colored equatorial planes of the ellipsoid
-fancy3 draw colored equatorial planes with a transparent bounding surface
-fancy4 draw longest principle axis of ellipsoid
-fancy5 for ORTEP lovers, draw ellipsoid with octant missing
-fancy6 for ORTEP lovers who want the missing octant to be a different 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 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 probability 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 0.10Å 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.

#### OPTIONS USED FOR STATISTICAL ANALYSIS

-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 (columns 77:78 in the PDB ATOM record) in the preparation of statistical summaries.

-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 104 Å2 x Uij , in the order U11, U22, U33, U12, U13, U23. Note in particular that the order of cross-terms is not the same as that used by ORTEP or SHELX, which do not use PDB format. However, the program shelxpro will produce correctly formatted PDB records from a SHELX coordinate file.

#### AUTHOR

Ethan A Merritt

#### REFERENCES

M.N. Burnett & C.K. Johnson (1996). "ORTEP-III: Oak Ridge thermal ellipsoid plot program for crystal structure illustrations". ORNL-6895, Oak Ridge National Laboratory. Table 6.1

K.N. Trueblood et al (1996). "Atomic Displacement Parameter Nomenclature, report of a subcommittee on atomic displacement parameter nomenclature". Acta Cryst. A52, 770-781.

E.A. Merritt (1999). "Expanding the Model: Anisotropic Displacement Parameters in Protein Structure Refinement". Acta Cryst. D55, 1109-1117. (Copyright © International Union of Crystallography).

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