Program features

Swiss PDV Viewer is a free program to display, analyse and manipulate PDB protein structures. Next to features such as protein superimposition, H-bond detection, amino acid mutation etc., the protein is tightly linked to Swiss- Model, an automated homology modelling server running at the Geneva Biomedical Research Center. This allows for threading a protein primary sequence to a 3D template and analysing homology. The displaying options of the program include spacefill, ball & stick, stick and ribbon representations, all of which can be applied simultaneously within one structure model.

In relation to molecular graphics, the feature that protein structures as represented on display in Swiss PDB can be exported as Povray (2.0 or 3.0) script files is the most important. Povray is a shareware ray-tracing package which is continuously in development and is available for most platforms. Here's a short description of the program, taken from the Povray 3.0 documentation:

'The Persistence of Vision(tm) Ray-Tracer creates three-dimensional, photo- realistic images using a rendering technique called ray-tracing. It reads in a text file containing information describing the objects and lighting in a scene and generates an image of that scene from the view point of a camera also described in the text file. Ray-tracing is not a fast process by any means, but it produces very high quality images with realistic reflections, shading, perspective and other effects.'

Although Swiss PDB Viewer is internally linked to the ray-tracing package Apple QuickDraw3D, which also allows for the generation of ray-traced images, the pictures generated with Povray are superior in quality by far. Moreover, the standard Swiss PDB export Povray script file can be changed to include all the ray-tracing features Povray offers, such as:

• Advanced texturing allowing objects to appear as metallic, transparent, glossy, dull etc.
• Atmospheric effects (fog, rainbows, skies, focal blur etc.).
• Spotlights, cylindrical lights and area lights for sophisticated (colored) lighting.
• Halos to model effects like clouds, dust, fire and steam.
• Large built-in library of object primitives (shapes), textures and texture patterns.
• Generation of images in any resolution up to 48 bit color depth.
• Automatic generation of animations.

Povray is a ray-tracing package only, which takes its information from Povray script text files. These script files have to be made elsewhere, as in Swiss PDB Viewer in the case of protein models. Next to Swiss PDB Viewer, several specialised modeling packages for making Povray scenes are available, like Moray 2.0 for Windows 95. This program offers a wide variety of modeling features to design complex objects, textures, lights etc., which can be merged with the Povray protein structure so as to create a complete scene. Moray does not read standard Povray script files, but uses its own storage format. Thus, the Swiss PDB export file can not be directly imported in Moray to work from there. Luckily, there exist Povray to Moray file format converters such as pov2mdl.exe. Unfortunately, the latter program only works when the Swiss PDB export file only contains spacefill or ball&stick models (the converter does not recognize the primitives used to describe strands and ribbon representations). Also, the Povray script file requires some manual editing prior to conversion to the Moray format file. When the Povray to Moray conversion does not work, it is always possible to merge the Swiss PDB and the Moray export files manually by making a new Povray script containing both source codes, although this can be a tricky process.

Using a seperate modeling program and changing the Povray script is not a prerequisite for obtaining nice images, though. Even the standard Swiss PDB Povray export format can yield satisfying results, since Swiss PDB Viewer itself includes options to change atom colors, alter stick thickness, positions and colors of lights, background color etc. Thus, a lot of picture tuning can be done without even touching the Povray script export file. Yet, when one wants to fully exploit the features offered by Povray, the Povray script language should be learned. Although such a script file seems difficult to understand at first glance, reading the Povray documentation and working through the basic tutorials provide a good handle on this (tip: when editing script files in Povray, positioning the cursor on a particular command and pressing Ctrl+F1 opens a context sensitive help window). After this, modifying script files and problem solving become intuitive and rather straightforward. Obviously, this is when designing images becomes fun! :-)