Connect_file [file_name]
Define a new connectivity file. A number of connectivity files are distributed. The file all.dat draws bonds between non-hydrogen atoms for all amino acid. The connectivity in file o.dat draws bonds between CA and all non-hydrogen sidechain bonds. File xplor.dat includes essential hydrogens. File trna.dat contains the connectivity for tRNA. The tRNA connectivity could be added to the amino acid connectivity if desired. Any residues not described in the connectivity file have bonds drawn according to a distance criterion.
The format of the connectivity file is simple. The LINK statement specifies the maximum separation between atoms in adjacent residues for a bond to be drawn. For each residue, there is a number of records. The first one contains the name (type) of residue. Subsequent records start with the keywords ATOM or CONNECT. The ATOM records specify the names of the atoms making up the residue. Each CONNECT record specifies a linked list of bonds between atoms. The connections to the previous and next residues are specified by - and +. These special connections must occur on the same CONNECT record. Below is an example of the entry for Valine:
VAL ATOM N CA C O CB CG1 CG2 CONNECT - N CA C + CONNECT CA CB CG1 CONNECT CB CG2 CONNECT C O
The atom names associated with each residue are also used with the Sam_init_db command to generate database entries corresponding to a particular sequence.