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29.1.6 peer — Interactive Molecular Display Program

peer is a simple graphics program for "peering" into a set of molecule. It can also be used to manipulate the molecules orientation with respect to one another in a very crude way.

The fundamental operation of the program is to display the molecule using either vector or space filling representations. Transparent spheres are also supported. You can move or rotate the view at will using the dials or the keyboard. The program's input file specifies the molecules by their atoms and bonding connections. Up to 32 molecules can be read in. These molecules can be selected using the buttons, and when they are selected, they can be moved relative to the non-selected molecules.

Not all of these features of this program can be used on Personal Irises. In particular, anti-aliased vectors, depth-cued vectors, and transparent spheres are not supported on PI's.

The peer file is normally generated by the peer command in CONGEN, see Peer Command. It is a text file and describes of a set of molecules, each of which is given in three parts. Each of the parts consists an initial line count which is on a line by itself followed that many lines. The first part of molecule is the color table. Only the color table of the first molecule is used. Next comes a list of atoms specifying the segment id, residue name, residue id, IUPAC atomic name, XYZ coordinates, radius, and color. Finally, a list of bond connections is given, one per line where each bond connection is specified by atom numbers. In principal, such a specification could be made by hand.

There are two major modes of operation for peer, one where no molecules are selected, the other when some are. The difference between these two modes is the intepretation of the dials as we shall describe below.