Raster3D Frequently Asked Questions

(last change: 20 Jun 2003)

Topics covered:

What machines does Raster3D run on?

Raster3D is distributed as source code (mostly Fortran, with a few C routines), so it should run on anything that has Fortran and C compilers installed. You wouldn't believe how many strange compilers are out there, however, so I can only promise smooth installation on machine configurations which I have tested myself. That means mostly unix boxes, including those from DEC/Compaq/HP (DU4, Tru64), SGI (Irix), and IBM (AIX).

The source distribution builds smoothly under linux. I am also now providing RPM packages of the source and binaries compiled with the pgf77 optimizing compiler. These pre-compiled binaries run approximately 20% faster than you would get using g77/gcc.

Raster3D does not depend on graphics hardware of any sort.

Yeah OK, but what about a PC or MAC version?

Windows

Many thanks to Suhaib Siddiqi, who has contributed a set of Windows binaries for version 2.6c.

MacOSX

Raster3D has been ported to MacOSX by the GNU-Darwin project. It is part of the base installation, so if you are a One Step installer user, then you already have it. For further information on GNU-Darwin see http://www.gnu-darwin.org

What is the current version?

The most recent version being distributed is Version 2.7b (20 Jun 2003). Here are the Release Notes.
However the label3d and stereo3d scripts in 2.7b are incompatible with versions of ImageMagick and libtiff found in some older linux distributions. If you run into this problem, try version 2.6e

What other programs will produce Raster3D input files?

Raster3D is distributed with several utility programs (notably balls and rods) for creating input files directly from PDB format atomic coordinate files. You can read about these in the Raster3D manual. Other programs which are capable of generating files used by Raster3D include:

Can I keep Molscript labels in my Raster3D picture?

Yes, it is possible to keep the labels from a Molscript V1.4 picture when you convert it to Raster3D. I don't recommend this procedure, but here is a summary of how to do it if you really want to.

Molscript V2 is a whole other story, and can pass through labels to Raster3D by itself.

How can I position stereo labels?

With difficulty (sorry). See the above procedure to transfer Molscript labels to Raster3D. What I do is to bring the full-size (usually larger than one screen) image into GIMP and just type the labels onto it.

Molscript V2 is again a different story; these labels will become stereo automatically along with the rest of the image.

More label options?

Raster3D does contain label support now, including stereo labels. The problem is that not many of the higher level programs have been modified to pass the label information through to Raster3D. Here is a little MPEG animation demonstrating labels generated using the Raster3D utility label3d.

How can I make stereo pairs?

There is a utility program in Raster3D called stereo3d. It will take any [mono] input file to render, and produce a side-by-side stereo pair of the same scene.

Can I have more than two light sources?

You can have additional non-shadowing light sources. These are specified as objects using a new object type GLOWLIGHT (type 13).

How do you make the background white rather than black?

Each input file to the render program starts with 19 header records that describe image layout and processing options. The fifth line contains three numbers which specify the RGB values for the background. 0 0 0 specifies a black background; 1 1 1 specifies a white background; 0.9 0.9 0.4 specifies a light yellow background, and so on.

Why does my picture look all jaggedy when I convert it to PostScript?

The first thing you have to realize is that there is a fundamental difference between a raster image (which is what Raster3D produces) and a PostScript file. The PostScript language is designed to describe characters, lines, and shapes in terms of coordinates on a page of a certain physical size. A raster image knows nothing about characters, lines, shapes, or pages of any size; it's just a bunch of colored dots (pixels). It is possible to describe a pixel dump in PostScript, but unless you are extremely careful the image quality may degrade substantially.

Rule 1:

Do not convert a raster image into PostScript unless you really, really have to.
The only time this should happen is if you need to send the image to a printer that understands nothing but PostScript.

Rule 2:

You must know the exact size of your image in pixels and the physical resolution of the PostScript device (your printer) in pixels-per-inch.
If you want to print the image on a device with a different resolution you will have to do the conversion all over again.

Rule 3:

You will have to do it by hand.
Since for obscure historical reasons PostScript conversion programs all assume that the output device resolution is 72 dpi (dots-per-inch), and since no printer I have ever seen really has this resolution, automatic conversion of your beautiful image into PostScript is not likely to work.

In case of true need, here is how to convert your image to PostScript using ImageMagick

What happened to TIFF support? I get these error messages....

TIFF support has fallen victim to the Unisys claim of patent rights covering the use of LZW compression. Because of these claims, distributed versions of the TIFF library (libtiff.so) no longer allow compression. This makes TIFF pretty useless as an image format, so all Raster3D programs and scripts have been modified to create PNG images by default. However, communication between other programs (e.g. Xfit) and Raster3D may still use intermediate TIFF images, which can cause a problem.

To work around this problem in Xfit:


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Ethan A Merritt / merritt@u.washington.edu / Biomolecular Structure Center at UW