Three-dimensional cues for a molecular computer graphics system

The perception of depth in three-dimensional objects presented on a two-dimensional display can be enhanced by many techniques. This thesis develops programs for implementing a number of such techniques flexibly and efficiently, including rotation, intensity modulation, and stereo. These techniques are applied to the GRIP-75 molecular computer graphics system with which crystallographers fit proteins or nucleic acids to their electron density maps. A fragment of a molecule is superimposed on a contoured electron density map and presented to the user for manual manipulation. My thesis is that motion decomposition pervades surprisingly many aspects of our computer-graphics-guided manual manipulation, that smooth rotation appears to be the single best depth cue currently available, that a variety of multiple image effects, due to disparity between refresh and update rates, can plague moving pictures, that the good 3-D perception provided by stereo can hinder manipulation, and that achieving orthogonality among functions is surprisingly important and difficult. The programs run on a satellite graphics system consisting of a DEC PDP-11/45 computer driving a Vector General display system, and a high-speed selector channel which provides communication with a time-shared host computer, an IBM System/360 Model 75. The programs developed are written in PL/I and reside mainly in the satellite.