The Amiga 3000 is nearly ideal for desktop molecular modeling. It uses the Motorola 68030 32-bit processor, running at 16 or 25 MHz, with either the 68881 or 68882 math coprocessor and eight custom processing chips. The video system is NTSC compatible 15.75- or 31.5-KHz RGB analog or digital. The system video interface offers user selectable 320 x 200, 640 x 480, 768 x 480 or 1280 x 400 resolution with a displayable palette of 4,096 colors and interlaced, noninterlaced and overscan modes. NTSC compatibility permits simple and inexpensive video signal synchronization, so that composed monitor images can be displayed and recorded with standard video equipment. The processor, in conjunction with the custom video chips, can manipulate models mathematically at a sufficient rate to present moving or animated images in real time. Users can interact with the molecular image with mouse or joystick controls. A third-party manufacturer, Haitex Resources, has produced an inexpensive stereo image display interface for the Amiga. This stereo image display system consists of liquid crystal shutter goggles attached to a control module on one mouse/joystick port and synchronized at 60 Hz with alternating left/right screen displays. Several simple molecular graphics programs for the Amiga have been available in the public domain since 1988. The ease of video interfacing and the availability of stereo image display have stimulated several developers to begin assembling molecular modeling packages. At the National Biomedical Research Foundation the Amiga is being tested as an inexpensive stereo-image color graphics workstation for molecular modeling, biopolymer sequence analysis and medical imaging.(ABSTRACT TRUNCATED AT 250 WORDS)