Simulation and display of macromolecular complexes

An interactive program for building, manipulating and displaying molecules has been written. The program provides perspective, planar, and stereoscopic views on a computer terminal display. The views are given both for standard observer locations relative to the object and for locations determined and varied by the user. The user can rotate the whole molecule or parts of it relative to any axis in space, which can also be one of the bonds. The whole molecule or parts of it can be translated in a given direction and bond connections can be added or eliminated by the user. One of the subroutines enables juxtaposition of two molecular fragments in such a fashion that two given bonds are aligned and two planes and two corresponding points coincide. Hence the user can join two molecular fragments at a sought relative orientation and location. Another option includes a duplication of a given unit, e.g. an amino-acid or a DNA base. The program is running on the Roswell Park Univac 70 Computer which employs a time sharing system, but it has been written with an emphasis on flexibility and an easy adaptability to any computer. The display at the Roswell Park computer is supported by a hard copy unit, but plotter drawings can also be generated. The program is written in FORTRAN. In our laboratory the program is employed as one of the tools in the study of template properties of polynucleotides and their specific interactions with polypeptides. Few examples are illustrated.