rastep - (Raster3D Thermal Ellipsoid Program)

            Ethan A Merritt.

Raster3D                                           14 Dec 2010                                         RASTEP(1)

       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

       rastep - (Raster3D Thermal Ellipsoid Program)

       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.

-auto

       Auto-selection of viewing angle, chosen to minimize the spread of the atoms along the view direction.

       -BcolorBminBmax

       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.

       -probPlevel

       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.

       -radiusR

       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.

       raster3d(l), render(l)

webURL:http://www.bmsc.washington.edu/raster3d/raster3d.htmlcontact:
             Ethan A Merritt
             University of Washington, Seattle WA 98195
             merritt@u.washington.edu

rastep[-h][-iso][-BcolorBminBmax][-probPlevel][-fancy[0-3]][-radiusR]<infile.pdb>ellipsoids.r3drastep-tabulate[tabfile][-by_atomtype][-com[comtabfile]]<infile.pdb>statistics.textRastep 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.