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26.2 PEER Command

The PEER command is used for generating input files to the peer program, see Peer, for a complete description.

26.2.1 Syntax

     PEER UNIT unit [RADIus real] [SEQLink] atom-selection

The atom-selection is described in Atom Selection.

26.2.2 Function

Each invocation of the PEER command generates a single object for use by peer. The object consists of three parts; a list of colors, a list of atoms, and a list of bonds. The colors come from the SPHERE command. The atoms are selected from atom-selection you specify in the command, and only atoms which have defined coordinates are eligible for inclusion into the object. The bonds can be specified in two ways. If you omit the SEQLINK option, then only bonds between selected atoms are included. If you include the SEQLINK option, then a bond is drawn between each selected atom. This latter option is useful for making alpha-carbon displays. The object is written to the file on the unit you specify with the UNIT operand. It is a formatted file, and if multiple PEER commands are issued to the same unit in a CONGEN run, each object will be appended to the file. Note that only the first color table is used by peer.

Before using the PEER command, you must first invoke the SPHERE command, see Usage of Sphere Drawing. It suffices just to enter the command, and then leave it. For example,


The SPHERE command defines the color table, as well as specifying a default color for all the atoms in the system.

Normally, atomic radii are specified by the parameter set as the van der Waals radii. However, if the RADIUS option is used, then you can specify the radii of all the atoms explicitly. Do not specify a negative or zero radii, as CONGEN will interpret this to mean that the van der Waals radii should be used.