Description
Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.
Raster3D was developed at the University of Washington. Raster3D website.
Raster3D is intended to be used on Helix. To run a Raster3D job, log on to helix.nih.gov using ssh, initialize the program as described below, and then type in the name of any Raster3D command.
Version
How to Use
Before running a Raster3D command, type the following:
source /usr/local/raster3d/Raster3D.csh (csh or tcsh users)
source /usr/local/raster3d/Raster3D.sh (bash users)Example 1: Running Raster3d interactively and displaying the image.
You will need an X-Windows connection to helix for the image to display on your desktop machine.
User input in bold:
[user@helix ~]$ source /usr/local/raster3d/Raster3D.csh [user@helix ~]$ gunzip -c /fdb/pdb/ey/pdb2eyd.ent.Z | ribbon -d2 > ribbon.r3d No view matrix or angles provided 92 atoms accepted from input. No colours in input. X min max: -8.02 7.71 Y min max: -13.97 15.76 Z min max: -7.76 10.13 scale: 33.03 color scheme 2 0.000 0.000 0.400 0.500 0.000 0.000 0.600 0.600 0.600 Ribbon drawn with 2 strands, width 1.50A Number of chords = 5, offset = 1.20A [user@helix ~]$ vi ribbon.r3d (to set background to white) [user@helix ~]$ cat ribbon.r3d | render | display png:- title="C-alpha ribbon - Raster3D V2.7d" Rendered raster size = 960 x 768 Output raster size = 640 x 512 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Raster3D V2.7d % % -------------------------------------- % % If you publish figures generated by this program please cite % % Merritt & Bacon (1997) Meth. Enzymol. 277, 505-524. % % -------------------------------------- % % Raster3D distribution site % % http://www.bmsc.washington.edu/raster3d/ % % comments & suggestions to: merritt@u.washington.edu % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% To center objects in rendered scene, change translation to: 0.2575 -0.2895 -0.7910 Z limits (unscaled) before clipping: -8.82 9.28 Z-clipping limits: -33.07 none ------------------------------- plain triangles = 2 ribbon triangles = 382 total objects = 384 ------------------------------- rendering time - 0 sec
Example 2: sphere model of sugars, jpeg image.
Image written to a file and then displayed via the ImageMagick program suite.
[user@helix ~]$ cat sugars.pdb | balls | render -jpeg > sugars.jpg No view matrix or angles provided title="balls - Raster3D V2.7d" Rendered raster size = 960 x 768 Output raster size = 640 x 512 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Raster3D V2.7d % % -------------------------------------- % % If you publish figures generated by this program please cite % % Merritt & Bacon (1997) Meth. Enzymol. 277, 505-524. % % -------------------------------------- % % Raster3D distribution site % % http://www.bmsc.washington.edu/raster3d/ % % comments & suggestions to: merritt@u.washington.edu % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% X min max: 2.26 71.26 Y min max: 57.20 98.91 Z min max: 18.80 83.98 scale: 61.34 To center objects in rendered scene, change translation to: -36.7605 -78.0545 -51.3905 Z limits (unscaled) before clipping: -27.59 35.60 Z-clipping limits: -61.42 none ------------------------------- spheres = 340 total objects = 340 ------------------------------- rendering time - 0 sec [user@helix ~]$ display sugars.jpg
Example 3: Using Molscript to produce the Raster3d file.
[user@helix ~]$ molauto 1ze0.pdb > 1ze0.in [user@helix ~]$ molscript -r < 1ze0.in | render -png > 1ze0.png ----- MolScript v2.1.2, Copyright (C) 1997-1998 Per J. Kraulis ----- ref: P.J. Kraulis, J. Appl. Cryst. (1991) vol 24, pp 946-950 ----- http://www.avatar.se/molscript/ reading PDB file... 162 residues and 1130 atoms read into molecule mol 1130 atoms selected for position 1130 atoms selected for transform rotation matrix applied: 1.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 1.00000000 translation vector applied: -37.4446 -39.5403 -35.7976 coil from A-8 to A0 (9 residues) helix from A0 to A12 (13 residues) [...] setting window to 41.96 setting slab to 32.45 880 triangles, 0 spheres and 677 cylinders. title="render (Raster3D) input file, MolScript v2.1.2, Copyright (C) 1997-1998 Per J. Kraulis" Rendered raster size = 750 x 750 Output raster size = 500 x 500 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Raster3D V2.7d % % -------------------------------------- % % If you publish figures generated by this program please cite % % Merritt & Bacon (1997) Meth. Enzymol. 277, 505-524. % % -------------------------------------- % % Raster3D distribution site % % http://www.bmsc.washington.edu/raster3d/ % % comments & suggestions to: merritt@u.washington.edu % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ----- MolScript v2.1.2, Copyright (C) 1997-1998 Per J. Kraulis ----- ref: P.J. Kraulis, J. Appl. Cryst. (1991) vol 24, pp 946-950 ----- http://www.avatar.se/molscript/ To center objects in rendered scene, change translation to: 0.8200 -0.5850 -0.4600 Z limits (unscaled) before clipping: -15.18 16.10 Z-clipping limits: -42.02 none ------------------------------- cylinders = 564 plain triangles = 46 surface triangles = 834 hidden surfaces = 322 total objects = 2324 ------------------------------- rendering time - 0 sec [user@helix ~]$ display 1ze0.png
Documentation
Online documentation at the Raster3d website.
FAQ at the Raster3d website.
