Difference between revisions of "checkchain.pl"
Revision as of 14:20, 12 August 2006
usage: checkchain.pl [-v] [chainFile]
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.
- usage information
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