1 .ad l 2 .nh 3 .TH RASTEP 1 " 14 Dec 2010" "Raster3D" 4 5 .SH NAME 6 7 rastep - (Raster3D Thermal Ellipsoid Program) 8 .SH SYNOPSIS 9 .PP 10 .B "rastep" [\fI-h\fP] [\fI-iso\fP] [\fI-Bcolor Bmin Bmax\fP] 11 .B [\fI-prob Plevel\fP] [\fI-fancy[0-3]\fP] [\fI-radius R\fP] 12 .B < infile.pdb > ellipsoids.r3d 13 .PP 14 .B "rastep" \fI-tabulate [tabfile]\fP [\fI-by_atomtype\fP] 15 .B [\fI-com [comtabfile]\fP] < infile.pdb > statistics.text 16 .PP 17 \fIRastep\fP reads a PDB coordinate file. 18 This file must contain ANISOU records describing atoms refined anisotropically. 19 \fIRastep\fP can either create an input file for the Raster3D render program 20 or perform a statistical analysis of the atomic anisotropy for various classes 21 of input atoms. 22 By default the program creates an ellipsoid+stick scene description in which 23 each atom is represented by an ellipsoid enclosing an isosurface 24 of the probability density function. 25 These are commonly known as thermal ellipsoids. 26 .PP 27 The program can be run in an alternate mode, controlled by the -tabulate option, 28 in which the primary output to stdout is a list of the Eigenvalues of the Uij 29 matrix, followed by the corresponding atomic anisotropy and isotropic Ueq, 30 for each atom in the input file with both an ATOM record and a 31 matching ANISOU record. 32 This mode is used by the validation tools Parvati and Skittls. 33 .PP 34 .SH EXAMPLES 35 .PP 36 To describe thermal ellipsoids at the 50% probability level, with default CPK 37 colors, and send it for immediate rendering into a PNG file 38 .PP 39 rastep < infile.pdb | render -png picture.png 40 .PP 41 To describe the same ellipsoids colored by Biso, omiting header records so that 42 the resulting input file can be merged with other scene components 43 .PP 44 rastep -h -Bcolor 10. 30. < infile.pdb > ellipsoids.r3d 45 cat header.r3d ellipsoids.r3d otherstuff.r3d | render > picture.png 46 .SH OPTIONS 47 48 .B "-auto" 49 .PP 50 Auto-selection of viewing angle, chosen to minimize the spread of the atoms 51 along the view direction. 52 53 .B "-Bcolor Bmin Bmax" 54 .PP 55 Assign colors based on B values rather than mathcing ATOM records against 56 input or default COLOUR records. Atoms with B <= Bmin will be colored 57 dark blue; atoms with B >= Bmax will be colored light red; atoms with 58 Bmin < B < Bmax will be assigned colors shading smoothly through the 59 spectrum from blue to red. 60 61 .B "-fancy[0-6]" 62 .PP 63 The \fI-fancy\fP option selects increasingly complex representations of 64 the rendered ellipsoids. 65 -fancy0 [default] = solid surface 66 -fancy1 = principal axes of ellipsoid, with transparent bounding surface 67 -fancy2 = colored equatorial planes of the ellipsoid 68 -fancy3 = colored equatorial planes with transparent bounding surface 69 -fancy4 = transparent bounding surface containing longest principle axis 70 -fancy5 = for ORTEP lovers, a solid ellipsoid with one octant missing 71 -fancy6 = for ORTEP lovers who want the missing octant in a separate color 72 73 .B "-h" 74 .PP 75 Suppress header records in output. 76 By default \fIrastep\fP will produce an output file which starts with 77 header records containing a default set of scaling and processing 78 options. 79 The \fI-h\fP flag will suppress these header records. 80 This option is useful for producing files which describe only part 81 of a scene, and which are to be later combined with descriptor files 82 produced by other programs. 83 84 .B "-iso" 85 .PP 86 Force isotropic probability surfaces (spheres). By default rastep will look 87 for ANISOU records in the PDB file and use these to generate ellipsoids. 88 If no ANISOU record is present for a given atom, the B value given in the 89 ATOM/HETATM record will be used to generate a sphere instead. Selecting the 90 \fI-iso\fP option will force the program to use the B value in the ATOM 91 record even if an ANISOU record is also present. 92 93 .B "-mini" 94 .PP 95 Auto-orientation (as in -auto) and small size plot (176x208). 96 97 .B "-nohydrogens" 98 .PP 99 Do not plot hydrogens, even if present in PDB file. 100 101 .B "-prob Plevel" 102 .PP 103 By default, isosurfaces are drawn to enclose the 50% probability level in the 104 density function described by the Uij values in the ANISOU record. 105 The \fI-prob\fP option allows you to select a different probability level 106 instead. If 0 < Plevel < 1 this value is interpreted as a fraction; 107 if Plevel > 1 this value is interpreted as a percent. 108 109 .B "-radius R" 110 .PP 111 By default, rastep draws bonds with radius 0.10A between neighboring atoms 112 using the same algorithm as rods. This option allows you to change the 113 radius of the bonds. If the radius is set to 0 no bonds are drawn. 114 115 .B "-tabulate [tabfile]" 116 .PP 117 The -tabulate option requests that the program accumulate and print 118 statistics on the distribution of anisotropy among atoms in the input 119 file rather than producing an input file for render. The principle axes 120 and anisotropy of each atom are written to stdout. An overall 121 statistical summary is written to tabfile if specified, otherwise to 122 stdout. 123 124 .B "-by_atomtype" 125 .PP 126 The -by_atomtype option is a modifier to -tabulate. It causes a further 127 subdivision of atoms by atom type in the preparation of statistical 128 summaries. Atom types are taken from columns 77:78 of the PDB ATOM 129 records. 130 131 .B "-com [comtabfile]" 132 .PP 133 Tabulate distribution of anisotropy in shells by distance from 134 center-of-mass. Output to comtabfile if specified, otherwise to stdout. 135 136 .SH NOTES 137 .PP 138 There is little, if any, consistency in format among the various programs 139 which write out anisotropic displacement parameters. This program interprets 140 the Uij values in the order specified for ANISOU records in PDB format. 141 That is, columns 29-70 of the PDB record are interpreted as integers 142 representing 10000 * Uij, in the order U11 U22 U33 U12 U13 U23. 143 Note in particular that the order of the cross-terms is not the same as that 144 used by ORTEP or shelx, neither of which use PDB format anyway. 145 However, the program shelxpro will produce correctly formatted PDB records 146 from a shelx coordinate file. 147 148 149 .SH SOURCE 150 .B web URL: 151 http://www.bmsc.washington.edu/raster3d/raster3d.html 152 .B contact: 153 Ethan A Merritt 154 University of Washington, Seattle WA 98195 155 merritt@u.washington.edu 156 157 .SH SEE ALSO 158 raster3d(l), render(l) 159 .PP 160 .SH AUTHORS 161 Ethan A Merritt. 162 163