genrestr.pl

Usage

usage:   genrestr.pl [option]
options: [-r min:max_force[=...]]
         [-l force min:max[=...]]
         [-seq file]

Show source

Description

Generates a positional restraint file for use with MONSSTER. The restraints can be specified either explicitly with -r or implicitly with -l. The -r option is followed by a list of residue ranges with a force constant. This list is translated directly into the corresponding restraint file.

The option -l is more useful for loop and fragment modeling. It requires the the maximum force constant and a list of residues that are not supposed to be restrained as arguments. Using these parameters restraints for the other residues are generates with force constants that increase smoothly from the beginning and end of the unrestrained regions as well as the beginning and end of the whole sequence. A MONSSTER sequence file has to be provided with -seq when the option -l is used. It may also be given with the -r option for translating the residue numbering accordingly.

Options

-help: usage information
-r min:max_force[=...]: generate harmonic restraint force for given residue range with given force constant
-l force min:max[=...]: generate harmonic restraints outside the specified residues range with given force constant
-seq file: provide sequence file for residue number translation

Examples

genrestr.pl -r 10:13_1.2=14:21_2.0
generates a MONSSTER restraint file with two sets of restraints: the first set applies to residues 10 through 13 with a force constant of 1.2, the second one to residues 14 through 21 with a force constant of 2.0

   12
   10  1.20000
   11  1.20000
   12  1.20000
   13  1.20000
   14  2.00000
   15  2.00000
   16  2.00000
   17  2.00000
   18  2.00000

...

genrestr.pl -seq 1vii.seq -l 1:36 1.2 10:21
generates MONSSTER restraints for all residues from 1 to 36 excluding the range 10 through 21 with a variable force constant of up to 1.2.