PovChem

Combining chemistry, ray tracing, and a little art to make high-quality molecular graphics

PovChem version 2, with an improved graphical user interface, is now available! Follow this link to find out more!

PovChem version 1.00 is still available for free here! Check out the WWW PovChem Manual for information on downloading the latest version. You may want to look at this manual page for more information on PovChem's features, machine support, distribution info, etc.

I used this software to create the image on the cover of the Feb 23rd, 1996 issue of Science magazine!

You may also be interested in my new vrml2pov program that can convert VRML files created with chemical programs like Molscript and Ribbons into POV format for high-quality rendering.

Blatant self-promotion: Please note that I do freelance custom molecular graphics work, so if you need a high-quality chemically-themed picture or animation, please visit my Custom Chemical Graphics page.

(Note! I am working on a DNA picture gallery! The images there are more artistic and are thus separated from this functional tour of PovChem.)

PovChem's Main Features

New in version 1.0:

Full support for animation sequences.
Full support for stereo pair generation.
A user-modifiable configuration file to streamline the many available options. (And no more compile-time options!)
Preview mode and basic image manipulation to allow the view to be set up precisely without having to edit the output files directly.
User-modifiable periodic table, to tailor color and radius of any element.
Improved symbolic definitions in the POV-Ray scene, to make it easy to understand and customize.
POV-Ray definitions re-worked to allow any object to be used as an atom or bond - for those who wish to get a bit creative!
Improved efficiency in run time, in the number of POV objects created, and in dynamic memory management.
Support for interface to other programs, such as graphical front-ends.

Previously available:

Takes PDB format molecules and creates a POV-Ray scene, fully compatible with POV-Ray 2.2 and up.
Three model types: CPK, Ball and Stick, and Cylinder.
Flexible coloring schemes for small molecules to large proteins.
Can search for and display hydrogen bonds.
MANY options to fine-tune the details of the molecular model.
Automatic view finder to fit the molecule into the whole screen.
Automatic light placement.
The POV-Ray scene generated is easy to modify to do quick changes in color or other details, and can be easily incorporated into other POV-Ray scenes.
The use of POV-Ray allows an image of any resolution to be created, for publication of anything from small figures to posters, in full 24-bit color.
Can be configured to call POV-Ray directly, and to call an image viewer to preview the images.

History and Motivation

It came to my attention, as a graduate student in organic chemistry, but also as one with a background in art and computer graphics, that there isn't much software out there that is easy to use for visualization of chemical structures. So, I wrote my own! The basic idea of taking molecular coordinates and feeding them to a raytracer is not new, and, in fact, there are other programs that do the same thing:

(If there are others, please let me know! I do not wish to slight anyone.) PovChem takes chemical information (in PDB format) and makes input to a terrific freeware package called Persistance of Vision Ray Tracer, which I will abbreviate as POVRay. Note: this is not an official POV Team product!

So why write this if something like it already exists? Well, I needed a program that could be easily used by my research group of organic chemists who know nothing of UNIX systems, command-line switches, or raytracers. I wanted a program that could be easily ported to any computer, by not relying on a heavily graphical interface. And I wanted to be able to tailor the models produced, playing with the color schemes, ball/cylinder radii, and most importantly for my group's research, I needed to do hydrogen bonds and stereo models. I needed something good for visualization of small molecules, not whole proteins (although it can do that, too). Plus, I enjoy programming, especially as a break from organic chemistry! So, in the true tradition of the hacker, I put together PovChem.

Your feedback is requested!

This program is not complete yet; at the moment, this web page serves as a preliminary advertisement, and more importantly, a way for you to tell me what other features you would like to see, and if you would be interested in using this software! I've released a version that is now available via the WWW PovChem Manual; please try this out and tell me what you think.

Finally, some graphics!

Below is a tour of the main features of PovChem. Caveats: Each small picture is a reference to a 640x480 file, so please be patient when downloading. Also, many of the files are 24-bit true color, and may look grainy and unsmooth with an 8-bit viewer. As these images were created on an SGI Indigo, they may require some gamma correction to look good on a PC or a Mac.

From Protein Data Bank entry 149d, a DNA triple helix, this is a simple CPK model. Notice the smooth shading and shadows. This picture took about 10 seconds to feed through PovChem, and about 5 minutes for POVRay to trace on a Silicon Graphics Indigo.

Raytracers are great, because you can use all sorts of interesting textures, such as metallic. Note the reflections!

This is a ball-and-stick model, with atoms colored by element and bonds coloring the three DNA strands. You can really see how the third strand in green fits into the major groove of the Watson-Crick duplex in red and blue.

Activate this image to get a cross-eyed (proximal) stereo picture of the above triplex - cross your eyes to combine the two images into one three-dimensional picture. You can also try the side-by-side (distal) version, "uncrossing" your eyes, if that's easier for you.

Here's the same model, plain cylinder bonds, looking down the axis of the helix. I've had PovChem look for hydrogen bonds; the Hoogsteen-type hydrogen bonds are between the green third strand and the red central strand, and the Watson-Crick hydrogen bonds are between the red and blue strands.

PovChem can do whole proteins, too. This is the heat-labile Enterotoxin (LT) from E. Coli, where the residues are colored in a spectrum along the primary sequence. There is a bound galactose and some water in the upper left corner, in red. (This image is a bit larger than the rest...)

Now for some smaller molecules... This is a model of a guanosine host that I made and studied as part of my Ph.D. research (see the Zimmerman group publications). It was designed to form 5 hydrogen bonds to a guanosine guest.

Now for some fun! Have you ever before seen a stone CPK molecule? :) With a very little knowledge of POVRay's control language, you can edit PovChem's output to do more artistic things...

... Or you can get even wilder!

Well, this page is already long enough... There are more examples in my DNA Gallery and my old research group's projects page. I hope this gives you a good idea of the range of things PovChem can do. If you think you might like to use it, please send me mail and I'll put you on the list of people that I'll notify about PovChem's release and version status. You can also see the WWW PovChem Manual for more specific info on features and where to get PovChem.

Thanks for your time!

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