RASTEP

(Raster3D Thermal Ellipsoid Program)

SYNOPSIS

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

rastep reads a Brookhaven PDB coordinate file and creates an input file for the Raster3d render program. Atoms are represented by ellipsoids enclosing an isosurface of the probability density function described by the Anisotropic Displacement Parameters Uij, commonly known as thermal ellipsoids.

EXAMPLES

To describe thermal ellipsoids at the 50% probability level, with default CPK colors, and send it for immediate rendering into a TIFF image file:

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

To 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 -tiff picture.tiff

OPTIONS

-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.
-Bcolor Bmin Bmax: Assign colors based on B values rather 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.
-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.
-fancy[0-3]: The -fancy option selects increasingly complex representations of the rendered ellipsoids (see figure below)

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 Å²x Uij , in the order U11, U22, U23, 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.

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