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.
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 -tiff picture.tiff
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
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
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.
![[figure]](rastep_options.gif)
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.
Ethan A Merritt
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".
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