MMTSB
Tool Set Documentation

checkchain.pl

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Usage

usage: checkchain.pl [-v] [chainFile]
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Description

Checks the validity of a SICHO model lattice chain for use with MONSSTER. To increase computational efficiency MONSSTER applies truncated distance-dependent potentials. This imposes restrictions on the lattice chain to fall within the limited distance intervals. The square of the distance between any two virtual particles has to be at least 9 and not larger than 30 between particles i and i+1 and 68 between particles i and i+2 along the chain. Furthermore, subsequent relative vectors between particles i, i+1 and between i+1, i+2 are not allowed to be colinear.

This script expects a lattice chain file as an argument or through standard input and reports any violations to standard output. The option -v may be used to request more detailed information about violations.

Options

-help 
usage information
-v 
detailed information about chain format violations

Examples

checkchain.pl 1vii.simple.chain
checks a chain file (generated with genchain.pl -s 1vii.exp.pdb) for violations with the MONSSTER format

3 violation(s) found in chain


checkchain.pl -v 1vii.simple.chain
checks a chain file (generated with genchain.pl -s 1vii.exp.pdb) for violations with the MONSSTER format and provides verbose output with more detailed information about each violation

residues  10 <->  34 are too close (8, min 9)
residues  11 <->  18 are too close (8, min 9)
residues  31 <->  32 are too far (33, max: 30)
3 violation(s) found in chain