next up previous contents index
Next: Requirements Up: Generating the Molecular Previous: Generating the Molecular

Syntax

<residue-number>
specifies the number of a residue, a four-character string that can include nonnumerical characters.
<segment-name>
specifies the name of a segment, a four-character string that can include nonnumerical characters.
SEGMent { <segment-statement> } END is invoked from the main level of X-PLOR.
<segment-statement>:==
CHAIn
{ [<chain-statement>] } END   generates a sequence of residues. The END statement activates the generation.
MOLEcule
NAME=<residue-name> NUMBer=<integer>
END
generates individual molecules such as in liquids (default of NUMBer is 1). The residue numbers are assigned sequentially, starting with 1. The residue name has to be defined in the topology statement (see Section 3.1.1). The END statement activates the generation of the molecules.
NAME=<segment-name>
specifies the segment name of all atoms to be generated using one of the following statements (default is `` ").

<chain-statement>:==
COORdinates { <pdb-record> } END
takes a sequence from a coordinate file. It interprets the atom records of a PDB coordinate file in terms of the sequence of the molecule. The residue numbers are taken directly from the PDB coordinate file; they do not have to be sequential. Note that this statement does not actually read the x,y,z coordinates. One should use the coordinate statement (Section 6.1) to read the coordinates. The segment name has to match characters 73 through 76 in the PDB coordinate file. (For the definition of <pdb-record>, see Section 6.1.)

FIRSt
<residue-name>
TAIL=<patch-character>=<*residue-name*> END
adds a special patch for the first residue in a sequence to the chain database. In the case of multiple statements, equality has priority before wildcard matching; i.e., the more special assignments come first. The chain database is reset each time the chain statement is invoked.

LAST
<residue-name>
HEAD=<patch-character>=<*residue-name*> END
adds a special patch for the last residue in a sequence to the chain database. In the case of multiple statements, equality has priority before wildcard matching; i.e., the more special assignments come first. The chain database is reset each time the chain statement is invoked.
LINK
<residue-name>
HEAD=<patch-character>=<*residue-name*>
TAIL=<patch-character>=<*residue-name*> END
  adds a special linkage patch to the chain database. The statement will automatically connect residue i to residue i+1; e.g., it creates a peptide linkage. Wildcards are allowed for residue name. In the case of multiple statements, equality has priority before wildcard matching; i.e., the more special assignments come first. The chain database is reset each time the chain statement is invoked.
SEQUence { <residue-name> } END
takes the sequence as specified between the SEQUence and the END word. The residue numbers are assigned sequentially, starting with 1.



next up previous contents index
Next: Requirements Up: Generating the Molecular Previous: Generating the Molecular



Sat Mar 11 09:37:37 PST 1995