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<title> Raster3D package for photorealistic molecular graphics </title>
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<br>
<h1 align=center>Raster3D V3.0</h1>
<br clear=all>
The Raster3D molecular graphics package consists of a core program
<a href="render.html">render</a>
and a number of ancillary programs that read atomic coordinates from
PDB (Protein Data Bank) files to produce scene descriptions for input to render.
Raster3D can also render images composed using other programs such as
Molscript, Xfit, and coot.
<div class="box">
<table noborder>
<tr valign=top>
<td>
<b>Index</b>
<ul>
<li><a href="http://www.bmsc.washington.edu/raster3d/r3d_FAQ.html">FAQ
(Frequently Asked Questions)</a>
<li><a href="#general">Synopsis</a>
<li><a href="#examples">Brief examples of use</a>
<li><a href="#source">Distribution site</a>
</ul>
</td>
<td>
<b> </b>
<ul>
<li><a href="#related">Related programs</a>
<li><a href="#authors">Authors</a>
<li><a href="#cite">Citing the program</a>
<li><a href="#refs">References</a>
</ul>
</td>
</tr>
<tr><td></td><td></td></tr>
<tr valign=top>
<td>
<b>Programs in the Raster3D package</b>
<ul>
<li><a href="avs2ps.html">avs2ps</a>
<li><a href="balls.html">balls</a>
<li><a href="label3d.html">label3d</a>
<li><a href="normal3d.html">normal3d</a>
<li><a href="rastep.html">rastep</a>
<li><a href="render.html">render</a>
<li><a href="ribbon.html">ribbon</a>
<li><a href="rings3d.html">rings3d</a>
<li><a href="rods.html">rods</a>
<li><a href="stereo3d.html">stereo3d</a>
</ul>
<b>Filters</b>
<ul>
<li>Import molecular surface descriptions from
<a href="r3d_filters.html#grasp">Grasp</a> or
<a href="r3d_filters.html#msms">MSMS</a>
</ul>
</td>
<td>
<b>Hints for composing pictures</b>
<ul>
<li><a href="r3d_animation.html">
Animation</a>
<li><a href="r3d_hints.html#black-white">
Black & White figures</a>
<li><a href="r3d_hints.html#clipping">
Clipping planes</a> and
<a href="r3d_hints.html#bounding">
Bounding planes</a>
<li><a href="r3d_hints.html#colors">
Colors</a>, and a
<a href="r3d_colorpicker.html">
<font color=#cc0000>C</font><font color=#ff00ff>o</font><font color=#0000cc>l</font><font color=#009900>o</font><font color=#996500>r</font> picking tool</a>
<li><a href="r3d_hints.html#composing">
Composing figures in other programs</a>
<li><a href="r3d_hints.html#matrix">
Coordinate systems</a>
<li><a href="r3dtops.html">
Labels</a> (special note:
<a href="r3d_hints.html#labels">
Molscript labels</a>)
<li><a href="r3d_hints.html#modularity">
Making your picture modular</a>
<li><a href="r3d_hints.html#shadowing">
Shadowing</a>
<li><a href="r3d_hints.html#stereo1">
Side-by-side figures and stereo pairs</a>
<li><a href="r3d_hints.html#output device">
Tailoring your image to the output device</a>
<li><a href="r3d_transparent.html">
Transparent surfaces</a>
<li><a href="r3d_examples.html">
Worked examples from the Raster3D distribution</a>
</ul>
</td>
<tr>
</table>
</div>
<h4><a name="general">SYNOPSIS</a></h4>
<p>
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 plus one matte channel.
</p>
<p>
Raster3D does not depend on graphics hardware. The rendering program currently
supports output to files in AVS, JPEG, TIFF, PNG and SGI libimage format.
To actually view or manipulate the images produced, you must also have installed
an image viewing package (e.g. John Cristy's ImageMagick or the SGI libimage utilities).
The Raster3D rendering program can be integrated with ImageMagick to
expand the flexibility of output formats and interactive use.
</p>
<p>
Ancillary programs are provided for the generation of object
descriptions based on atomic coordinates stored in PDB format.
Although Raster3D is not intended as a general purpose ray-tracing package,
nothing in the rendering process is specific to molecular graphics.
Some of the algorithms used have been chosen for speed rather than generality,
however. They work well for molecular graphics images, but possibly
would produce odd results if used for very different types of image.
</p>
<p>
Raster3D currently supports rendering six object types: spheres,
triangles, planes, smooth-ended cylinders, round-ended cylinders,
and quadric surfaces. It also supports the definition of material
properties (transparency, bounding planes, color, reflectivity)
that apply to groups of objects within the rendered scene.
</p>
<p>
New in version 3.0: Dynamic array allocation, direct rendering of
labels.
</p>
<!---
<h4><a name="history">HISTORY</a></h4>
<p>
Version 2.1 added support for additional "object types" which are
really modifiers for characteristic properties of existing objects.
These have since been expanded to include the specification of
explicit surface normals, colors, and transparency at the vertices
of the current object.
</p>
<p>
Version 2.2 added support for transparency.
</p>
<p>
Version 2.3 added support for
file indirection, additional anti-aliasing options, internal
light sources, and a separate alpha blend (matte) channel in the rendered image.
There is a new shell script, <a href="stereo3d.html">stereo3d</a>
to automatically generate a side-by-side stereo pair from a Raster3D input file.
</p>
<p>
Version 2.4 added support for
generalized quadric surfaces (ellipsoids, cones, etc).
Input lines beginning with '#' are treated as comments.
It introduced the utility program <a href="rastep.html">rastep</a>
which generates "thermal ellipsoid" representations of atoms based on the
Biso or Uij entries in a PDB file (ANISOU cards). The option of coloring
based on B values was added here and elsewhere.
</p>
<p>
Version 2.5 added support for Z-clipping, output to a JPEG image
file on stdout, piped output to ImageMagick for automatic conversion to
additional image types, and file indirection of header records.
It also upgraded support for handling labels (object types
10,11,12) using PostScript. See
<a href="r3dtops.html">r3dtops</a> and <a href="label3d.html">label3d</a>
documentation.
</p>
<p>
Version 2.6 added support for bounding planes, and removed the
previous limit on stacking transparent objects. The installation process
has been modified so that all user-configurable options are collected into
the files <i>parameters.incl</i> and <i>Makefile.template</i>.
</p>
<p>
<b>Version 2.7</b> changes the default output format to PNG for all programs.
</p>
--->
<h4>
<a name="examples">EXAMPLES</a></h4>
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-containing metalloprotein with a smoothly
shaded ribbon representation of the protein and spheres drawn for the Fe atoms:
<pre>
#
# 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 as AVS image file
#
cat ribbon.r3d irons.r3d | render > picture.x
</pre>
One can alternatively use Molscript to produce a Raster3D
input file by using the -r switch. Integrated use of
Molscript/Raster3D/ImageMagick allows one to describe, render, and view 3D
representations of existing Molscript figures.
<pre>
molscript -r < infile.dat | render | display png:-
</pre>
A similar example using xv as an image viewer, and assuming that
TIFF support has been built into the render program:
<pre>
molscript -r < infile.dat | render -tiff image.tif
xv image.tif
</pre>
The same image rendered as a side-by-side stereo pair:
<pre>
molscript -r < infile.dat | stereo3d -border -png stereo_pair.png
</pre>
The
Raster3D distribution also includes a filter utility which will convert the
24-bit color AVS output stream from render into a dithered black & white
PostScript image:
<pre>
render -avs < description.r3d | avs2ps > picture.ps
</pre>
<h4><a name="source">SOURCE</a></h4>
<dl>
<dt><i>via WWW: </i>
<dd><a href="http://www.bmsc.washington.edu/raster3d/raster3d.html">
http://www.bmsc.washington.edu/raster3d/raster3d.html</a>
<dt><i>contact: </i>
<dd>Ethan A Merritt
<br>Biomolecular Structure Center
<br>University of Washington
<br>merritt@u.washington.edu
</dl>
<h4><a name="related">RELATED PROGRAMS </a></h4>
<h5>Required for full installation:</h5>
<dl>
<dt>libgd
<dd>Generation of PNG and JPEG images, as well as label processing,
requires prior installation of the
<a href="http://libgd.org"><i>gd</i></a> graphics library.
libgd itself requires other libraries, but if you have libd itself
installed then you should be all set.
<dt>TIFF
<dd>In order to build in support for the direct output of TIFF image files,
you must separately obtain and install a copy of the TIFF library
(libtiff). However, you can only render text labels for PNG or JPEG
output, so you may be better off generating PNG images and then converting
them to TIFF afterward.
<dt>ImageMagick
<dd>For full functionality you should also obtain and install a copy of
<a href="http://ImageMagick.org"> ImageMagick</a>
</dl>
<h5>Some other programs with direct Raster3D output modes:</h5>
<dl>
<dt>Coot
<dd>The contents of the current view window in a Coot session may be rendered in
Raster3D using the <F8> hotkey. More complicated scripting from Coot
is also possible. Coot web page:
<a href="http://www.biop.ox.ac.uk/coot/">
http://www.biop.ox.ac.uk/coot/</a>
<dt>Molscript
<dd>Figures composed in Molscript can be rendered in Raster3D rather than
being printed as PostScript images. The Molscript web page is
<a href="http://www.avatar.se/molscript">
http://www.avatar.se/molscript</a>.
<dt>ORTEP and the small molecule world
<dd>ORTEX V7 (an interactive descendent of Carroll Johnson's ORTEP program)
now supports Raster3D as an output mode. ORTEX runs under DOS/Windows,
and is available from
<a href="http://www.nuigalway.ie/cryst/ortex.html">
http://www.nuigalway.ie/cryst/ortex.html</a>.
Another small molecule package running under Windows and incorporating
Raster3D rendering options is WinGX, available from
<a href="http://www.chem.gla.ac.uk/~louis/software">
http://www.chem.gla.ac.uk/~louis/software</a>.
<dt>VMD
<dd>Biomolecular visualization tool from the Theoretical Biophysics group
at the University of Illinois,
<a href="http://www.ks.uiuc.edu/Research/vmd/">
http://www.ks.uiuc.edu/Research/vmd/</a>
<dt>X3DNA
<dd>Figure generation and analysis tool for RNA and DNA structures.
X3DNA Web site:
<a href="http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html">
http://rutchem.rutgers.edu/~xiangjun/3DNA/</a>.
<dt>Xfit/XtalView
<dd> General crystallographic model building, map fitting, and
analysis program by Duncan McRee, available in both academic and
commercial versions,
<a href="http://www.sdsc.edu/CCMS/Packages/XTALVIEW/">
http://www.sdsc.edu/CCMS/Packages/XTALVIEW/</a>
</dl>
<br>
<h4>
<a name="license">LICENSE </a></h4>
Version 3 of the Raster3D package is distributed under the terms of
the <a href="http://www.perlfoundation.org/artistic_license_2_0">
Artistic License, Version 2.0</a>.
<h4>
<a name="authors">AUTHORS </a></h4>
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 modifications by Ethan A Merritt.
<h4><a name="cite">CITING THE PROGRAM</a></h4>
If you use the package to prepare figures for publication,
<i>please</i> give proper credit to the authors; the proper citation for the
most recent version of the package is Merritt & Bacon (1997) as given below.
<h4><a name="refs">REFERENCES</a></h4>
Bacon, D.J., & Anderson, W.F. (1988) ``A Fast Algorithm for Rendering
Space-Filling Molecule Pictures''. (abstract of paper presented at the Seventh
Annual Meeting of the Molecular Graphics Society). J. Molec. Graphics 6,
219-220. <br>
Kraulis, P.J. (1991) ``MOLSCRIPT: a program to produce both detailed and
schematic plots of protein structures''. J. Appl. Cryst. 24, 946-950.<br>
Merritt, E.A. & Murphy, M.E.P. (1994) ``Raster3D Version 2.0 - A Program
for Photorealistic Molecular Graphics''. Acta Cryst. D50, 869-873.<br>
Merritt, E.A. & Bacon, D.J. (1997) ``Raster3D
Photorealistic Molecular Graphics''. Methods in Enzymology 277, 505-524.<br>
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