normal3d(1) [debian man page]
NORMAL3D(1) General Commands Manual NORMAL3D(1) NAME
normal3d - apply transformation matrix in Raster3D input file SYNOPSIS
normal3d [options] < infile.r3d > normalized.r3d DESCRIPTION
normal3d reads a Raster3D input file from stdin, applies any coordinate manipulations specified in the header, and writes the modified file to stdout. The output file from normal3d describes exactly the same image as the original input file. Header records are left unchanged except for the transfomation matrix (which becomes the identity matrix) and the format specifiers (which are set to *). The -h flag suppresses all header records in the output file. All objects in the input file are also in the output file, but their coordinate descriptions have been normal- ized (i.e. the original transformation matrix has been applied). OPTIONS
-ang AA Only relevant for generating stereo pairs. By default stereo separation is created using a shear operator. The -ang option instead intro- duces an angular separation by rotating the left and right eye images by +/- AA degrees with respect to the original view angle. -expand In-line and normalize all instances of file indirection in the input stream. This results in a single input file containing no file indi- rection. The default is to simply copy file indirection lines (those begining with @) to the new input file without opening them or nor- malizing their contents. -h Suppress header records in output. This option is useful for producing files which describe only part of a scene, and which are to be later combined with descriptor files -size HHHxVVV Force the image size to HHH pixels horizontal and VVV pixels vertical. -stereo [scratch] This option causes the program to produce two additional files, left.r3d and right.r3d, that contain header records suitable for rendering the normalized object desctiption file as a side-by-side stereo pair. This option always suppresses header records in the primary output file. If a scratch directory name is given, it is prepended to give output files {scratch}_left.r3d and {scratch}_right.r3d SOURCE
web URL: http://www.bmsc.washington.edu/raster3d/raster3d.html contact: Ethan A Merritt University of Washington, Seattle WA 98195 merritt@u.washington.edu SEE ALSO
render(l), raster3d(l), stereo3d(l) AUTHORS
Ethan A Merritt. Raster3D 12 Dec 2010 NORMAL3D(1)
Check Out this Related Man Page
RIBBON(1) General Commands Manual RIBBON(1) NAME
ribbon - Raster3D molecular graphics package ribbon-drawer SYNOPSIS
"ribbon" [-h] [-d[0123456]] pdbfile or "ribbon" [-h] -d[0123456] - (to take PDB records from stdin) Ribbon reads a PDB coordinate file and produces a file on stdout containing Raster3D descriptor records for a ribbon representation con- structed from a triangular mesh. The file produced by ribbon may be fed directly to render or it may be combined with descriptor files produced by other Raster3D utilities. EXAMPLES
To describe a the entire protein chain as a single ribbon colored smoothly from blue at the N-terminus to red at the C-terminus: ribbon -d2 protein.pdb | render > chain_picture.png To color a multi-chain protein with specified colors for each chain: cat chaincolors.pdb protein.pdb | ribbon -d5 - > chains.r3d OPTIONS
-h Suppress header records in output. By default ribbon 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 so that the output file contains only triangle descrip- tors. 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. -d[0123456] By default ribbon requires interactive input to select ribbon parameters and coloring information. Five default coloring schemes are implemented, however, and these may be selected as a command line option to bypass any interactive input. -d or -d0 same as -d2 below -d1 solid color ribbon (defaults to blue) -d2 shade from blue at N-terminus to red at C-terminus -d3 one surface of ribbon is blue, other surface is grey -d4 shade front surface from blue to red, back surface is grey -d5 color separate chains using successive color cards from input stream. Note that pattern matching on the color records is _not_ done; colors are simply taken sequentially as new chains are encountered. -d6 Color by nearest CA atom as taken from the COLOUR records at the head of the input file DESCRIPTION
The input to ribbon consists of a single text file containing colour information [optional] and atomic coordinates in PDB data bank format. Only CA and carbonyl O atom records are required; all other input atoms are ignored. Ribbon parameters and colouring specified interac- tively when the program is run. Keyboard interaction may be bypassed by selecting one of the default colouring schemes using the -d flag. A triangular mesh ribbon is output as Raster3D descriptor records. By default the output file contains a set of header records as required by the render program. The header is constructed to include a TMAT matrix corresponding to the transformation matrix contained in file setup.matrix (if it exists), or to the Eulerian angles contained in file setup.angles (if it exists). Ribbon produces a continuous smooth trace of the protein backbone. For more complicated representations of protein secondary structure it is better to use a different program, e.g. MOLSCRIPT, rather than ribbon. ENVIRONMENT
The files setup.matrix and setup.angles, if they exist, affect the header records produced by ribbon. SOURCE
anonymous ftp site: ftp.bmsc.washington.edu web URL: http://www.bmsc.washington.edu/raster3d/raster3d.html contact: Ethan A Merritt University of Washington, Seattle WA 98195 merritt@u.washington.edu SEE ALSO
MOLSCRIPT(l), render(l), rods(l), balls(l) AUTHORS
Original ribbon code written by Phil Evans for the CCP4 version of FRODO. Modification to describe solid ribbons as triangular mesh for Phong shading in Raster3D package by Ethan A Merritt. Raster3D 8 May 1999 RIBBON(1)