raster3d(1) [debian man page]
Raster3D(1) General Commands Manual Raster3D(1) NAME
Raster3D - molecular graphics package SYNOPSIS
The Raster3D molecular graphics package consists of a core program render and a number of ancillary programs (balls, rastep, rods) which produce input files for rendering from PDB (Protein Data Bank) files of atomic coordinates. Raster3D can also render images composed using other programs such as MOLSCRIPT [Per Kraulis (1991), J. Appl. Cryst. 24, 946-950]. Raster3D is freely available. If you use the package to prepare figures for publication, please give proper credit to the authors. The proper citation for the current version is Merritt & Bacon (1997). Bacon & Anderson (1988) J. Molec. Graphics 6, 219-220. Merritt & Murphy (1994) Acta Cryst. D50, 869-873. Merritt & Bacon (1997) Meth. Enzymol. 277, 505-524. DESCRIPTION
Raster3D uses a fast Z-buffer algorithm to produce high quality pixel images featuring one shadowing light source, additional non-shadowing light sources, specular highlighting, transparency, and Phong shaded surfaces. Output is in the form of a pixel image with 24 bits of color information per pixel. Raster3D does not depend on graphics hardware. The following image output formats are supported: AVS, JPEG, PNG, TIFF, and SGI libimage. To actually view or manipulate the images pro- duced, you must also have installed an image viewing package (e.g. John Cristy's ImageMagick or the SGI libimage utilities). A filter utility avs2ps is included in the package which can convert an AVS format output stream directly to a dithered monochrome PostScript image. Although Raster3D is not intended as a general purpose ray-tracing package, nothing in the rendering process is specific to molecular graphics. EXAMPLES
Using only programs included in the Raster3D distribution one can create and render space-filling models, ball-and-stick models, ribbon models, and figures composed of any combination of these. The following set of commands would produce a composite figure of an Fe-contain- ing metalloprotein with a smoothly shaded ribbon representation of the protein and spheres drawn for the Fe atoms: # # Draw smooth ribbon with default color scheme 2, # save description (with header records) in ribbon.r3d # cat protein.pdb | ribbon -d2 > ribbon.r3d # # Extract Fe atoms only, and draw as spheres. # Color info is taken from colorfile. # Save description (with no header records) in irons.r3d # grep "FE" protein.pdb | cat colorfile - | balls -h > irons.r3d # # combine the two descriptions and render to a PNG image # cat ribbon.r3d irons.r3d | render > picture.png Integrated use of MOLSCRIPT/Raster3D/ImageMagick allows one to describe, render, and view 3D representations of existing MOLSCRIPT figures: molscript -r infile.dat | render | display png:- 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), rastep(l), rods(l), ribbon(l), balls(l), avs2ps(l), stereo3d(l) AUTHORS
Originally written by David J Bacon and Wayne F Anderson. Ancillary programs by Mark Israel, Stephen Samuel, Michael Murphy, Albert Berghuis, and Ethan A Merritt. Extensions, revisions, and modi- fications by Ethan A Merritt. Raster3D V3.0 14 December 2010 Raster3D(1)
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BALLS(1) General Commands Manual BALLS(1) NAME
balls - preprocessor for space-filling models in Raster3D molecular graphics package SYNOPSIS
balls [-h] Balls reads a file describing atom colours and/or a PDB coordinate file and produces a file containing Raster3D descriptor records for each atom in the input file. The file produced by balls may be fed directly to render or it may be combined with descriptor files produced by other Raster3D utilities. EXAMPLES
To describe a simple space-filling model coloured by residue type: cat mycolours.pdb protein.pdb | balls | render > mypicture.png To include a pre-selected view matrix with the same model: cp view1.matrix setup.matrix cat mycolours.pdb protein.pdb | balls | render > mypicture.png To prepend header records describing a pre-selected scale and view: cat mycolours.pdb protein.pdb | balls -h > balls.r3d cat header.r3d balls.r3d | render > mypicture.png OPTIONS
-h Suppress header records in output. By default balls 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 sphere 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. DESCRIPTION
The input to balls consists of a single text file containing colour information and atomic coordinates in PDB data bank format. Coordi- nates are output as Raster3D descriptor records with colours and sphere radii assigned according to the COLO records described below. By default atoms are assigned CPK colours. 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). Colours are assigned to atoms using a matching process, using COLOUR records prepended to the input PDB file. Raster3D uses a pseudo-PDB record type with with COLO in the first 4 columns: Columns 1 - 4 COLO 7 - 30 Mask (described below) 31 - 38 Red component 39 - 46 Green component 47 - 54 Blue component 55 - 60 van der Waals radius in Angstroms 61 - 80 Comments Note that the Red, Green, and Blue components are in the same positions as the X, Y, and Z components of an ATOM or HETA record, and the van der Waals radius goes in place of the Occupancy. The Red, Green, and Blue components must all be in the range 0 to 1. The Mask field is used in the matching process as follows. First the program reads in and stores all the ATOM, HETA, and COLOUR records in input order. Then it goes through each stored ATOM/HETA record in turn, and searches for a COLOUR record that matches the ATOM/HETA record in all of columns 7 through 30. The first such COLOUR record to be found determines the colour and radius of the atom. In order that one COLOUR record can provide colour and radius specifications for more than one atom (e.g., based on residue or atom type, or any other criterion for which labels can be given somewhere in columns 7 through 30), the "#" symbol is used as a wildcard. I.e. a # in a COLOUR record matches any character in the corresponding column in an ATOM or HETA record. All other characters must match literally to count as a match. Note that the very last COLO record in the input should have # symbols in all of columns 7 through 30 in order to pro- vide a colour for any atom whose ATOM/HETA record fails to match any previous COLOUR record. This idea of matching masks for colour speci- fications is due to Colin Broughton. Several files of COLOUR records, including one based on Bob Fletterick's "Shapely Models" and another mimicking CPK model parts, are pro- vided as samples. ENVIRONMENT
The files setup.matrix and setup.angles, if they exist, affect the header records produced by balls. 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
render(l), rods(l), ribbon(l) AUTHORS
Originally written by David J Bacon and Wayne F Anderson. Extensions and revisions by Ethan A Merritt. Raster3D 8 May 1999 BALLS(1)