Combining chemistry, ray tracing, and a little art to make high-quality
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
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
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
(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.
- 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.
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
History and Motivation
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
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.
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
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
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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This page and all its contents Copyrignt © 1995-2004 by Paul Thiessen / paul@ChemicalGraphics.com. All
rights reserved. Last updated
January 06, 2004.