Raster3D Frequently Asked Questions

(last change: 29 Mar 2014)

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.

The source distribution builds smoothly under linux. I am also now providing RPM packages of the source and binaries compiled with the Intel optimizing compiler as well as versions compiled with gfortran. The Intel versions run approximately 20% faster.

The Raster3D home page also has 32-bit executables for OSX 10.5. You may also be able to find executables in the Fink collection, although these may not be totally current. Or you can build from source.

Raster3D does not depend on graphics hardware of any sort.

Yeah OK, but what about a Windows version?


Many thanks to Suhaib Siddiqi, who contributed a set of Windows binaries for version 2.6c. Preparing a Windows build of Version 3.0 is in progress. If you can help, let me know.

What is the current version?

The most recent version being distributed is Version 3.0-3 (March 2014). Here are the Release Notes.

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.

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 short animation demonstrating labels generated from example 7 in the set distributed with Raster3D.

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?

The easiest way is to add an option to the render command line:
render -bg white < infile > figure.png

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 requires linking to an external library. Your local copy of the render may have been built without this. Either find another copy of the program that was linked to libtiff, or rebuild the render program yourself after first making sure you have the tiff library installed.

But converting from PNG to TIFF is easy. I recommend installing ImageMagick and using the command
convert fig.png fig.tiff
If you are doing this at the request of a publisher, they probably expect an uncompressed file. In this case use the command
convert -compress none fig.png fig.tiff

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