Molecular Graphics - Technology

Technology

Early interactive molecular computer graphics systems were vector graphics machines, which used stroke-writing vector monitors, sometimes even oscilloscopes. The electron beam does not sweep left-and-right as in a raster display. The display hardware followed a sequential list of digital drawing instructions (the display list), directly drawing at an angle one stroke for each molecular bond. When the list was complete, drawing would begin again from the top of the list, so if the list was long (a large number of molecular bonds), the display would flicker heavily. Later vector displays could rotate complex structures with smooth motion, since the orientation of all of the coordinates in the display list could be changed by loading just a few numbers into rotation registers in the display unit, and the display unit would multiply all coordinates in the display list by the contents of these registers as the picture was drawn.

The early black-and white vector displays could somewhat distinguish for example a molecular structure from its surrounding electron density map for crystallographic structure solution work by drawing the molecule brighter than the map. Color display makes them easier to tell apart. During the 1970s two-color stroke-writing Penetron tubes were available, but not used in molecular computer graphics systems. In about 1980 Evans & Sutherland made the first practical full-color vector displays for molecular graphics, typically attached to an E&S PS-300 display. This early color tube was expensive, because its was originally engineered to withstand the shaking of a flight-simulator motion base.

Color raster graphics display of molecular models began around 1978 as seen in this paper by Porter on spherical shading of atomic models. Early raster molecular graphics systems displayed static images that could take around a minute to generate. Dynamically rotating color raster molecular display phased in during 1982-1985 with the introduction of the Ikonas programmable raster display.

Molecular graphics has always pushed the limits of display technology, and has seen a number of cycles of integration and separation of compute-host and display. Early systems like Project MAC were bespoke and unique, but in the 1970s the MMS-X and similar systems used (relatively) low-cost terminals, such as the Tektronix 4014 series, often over dial-up lines to multi-user hosts. The devices could only display static pictures but were able to evangelize MG. In the late 1970s, it was possible for departments (such as crystallography) to afford their own hosts (e.g., PDP-11) and to attach a display (such as Evans & Sutherland's MPS) directly to the bus. The display list was kept on the host, and interactivity was good since updates were rapidly reflected in the display—at the cost of reducing most machines to a single-user system.

In the early 1980s, Evans & Sutherland (E&S) decoupled their PS300 display, which contained its own display information transformable through a dataflow architecture. Complex graphical objects could be downloaded over a serial line (e.g. 9600 baud) and then manipulated without impact on the host. The architecture was excellent for high performance display but very inconvenient for domain-specific calculations, such as electron-density fitting and energy calculations. Many crystallographers and modellers spent arduous months trying to fit such activities into this architecture.

The benefits for MG were considerable, but by the later 1980s, UNIX workstations such as Sun-3 with raster graphics (initially at a resolution of 256 by 256) had started to appear. Computer-assisted drug design in particular required raster graphics for the display of computed properties such as atomic charge and electrostatic potential. Although E&S had a high-end range of raster graphics (primarily aimed at the aerospace industry) they failed to respond to the low-end market challenge where single users, rather than engineering departments, bought workstations. As a result the market for MG displays passed to Silicon Graphics, coupled with the development of minisupercomputers (e.g., CONVEX and Alliant) which were affordable for well-supported MG laboratories. Silicon Graphics provided a graphics language, IrisGL, which was easier to use and more productive than the PS300 architecture. Commercial companies (e.g., Biosym, Polygen/MSI) ported their code to Silicon Graphics, and by the early 1990s, this was the "industry standard". Dial boxes were often used as control devices.

Stereoscopic displays were developed based on liquid crystal polarized spectacles, and while this had been very expensive on the PS300, it now became a commodity item. A common alternative was to add a polarizable screen to the front of the display and to provide viewers with extremely cheap spectacles with orthogonal polarization for separate eyes. With projectors such as Barco, it was possible to project stereoscopic display onto special silvered screens and supply an audience of hundreds with spectacles. In this way molecular graphics became universally known within large sectors of chemical and biochemical science, especially in the pharmaceutical industry. Because the backgrounds of many displays were black by default, it was common for modelling sessions and lectures to be held with almost all lighting turned off.

In the last decade almost all of this technology has become commoditized. IrisGL evolved to OpenGL so that molecular graphics can be run on any machine. In 1992, Roger Sayle released his RasMol program into the public domain. RasMol contained a very high-performance molecular renderer that ran on Unix/X Window, and Sayle later ported this to the Windows and Macintosh platforms. The Richardsons developed kinemages and the Mage software, which was also multi-platform. By specifying the chemical MIME type, molecular models could be served over the Internet, so that for the first time MG could be distributed at zero cost regardless of platform. In 1995, Birkbeck College's crystallography department used this to run "Principles of Protein Structure", the first multimedia course on the Internet, which reached 100 to 200 scientists.

MG continues to see innovation that balances technology and art, and currently zero-cost or open source programs such as PyMOL and Jmol have very wide use and acceptance.

Recently the wide spread diffusion of advanced graphics hardware, has improved the rendering capabilities of the visualization tools. The capabilities of current shading languages allow the inclusion of advanced graphic effects (like ambient occlusion, cast shadows and non-photorealistic rendering techniques) in the interactive visualization of molecules. These graphic effects, beside being eye candy, can improve the comprehension of the three dimensional shapes of the molecules. An example of the effects that can be achieved exploiting recent graphics hardware can be seen in the simple open source visualization system QuteMol.