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PURPOSE OF PROGRAM: Calculates inter-atomic distances between a (specified) source atom and all target atoms given a structure file in PDB format.

USAGE: disCal infile atom resnum [disCutOff] [-i]

COMMAND LINE ARGUEMENTS:

disCal: Name of the program

infile: Structure file in the "XPLOR PDB" format. Program considers only lines begginning with "ATOM" as atoms having cartesian coordinates - other lines are ignored (such as those containing keywords such as "REMARK" or "END". Column ranges and identities are assumed as follows:

Identity Column Range Data Type

Atom Designator (HA, etc) 1....4 String
Atom Index 6...10 Integer
Atom Type (Phe, Arg, etc) 12..15 String
Residue Type 18..20 String
Residue Number 22..26 Integer
X Coordinate 31..37 Float
Y Coordinate 39..46 Float
X Coordinate 48..54 Float
Occupancy 56..60 Float
B-factor 62..66 Float
Segment ID 73..76 String

atom: Specifies the name of the "source atom". It is either the name of an atom contained in the XPLOR PDB file or an xplor-type wild-card (such as HB# or HG*) Note * wildcards are only valid for LEU or VAL). In the case of # or * atom wildcards, averaging for all atoms designated by the # or * is active. Note that when using the * wildcard for atom designators, it must be enclosed in single quotes (in order to isolate this from the shell).

resnum: Specifies the residue number - Must fall within the range specified by the sequence.

OPTIONS:

-i: Specifies that intraresidue atoms be included in the search field. The default is to exclude such atoms from the search field.

disCutOff: Real number (in units of Angstroms) that specifies the radius of a sphere which rediates from a (specified) source atom. It determines whether a particular target atom is within a distance, d, of the source atom.
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Last updated on July 17, 2003