loopModel.pl

Usage

usage:   loopModel.pl [options] [PDBfile]
options:              [-loop inx:sequence[:secstr][=inx:sequence[:secstr]]]
                      [-models number]

Show source

Description

This script uses Modeller to build missing loops in a given PDB structure.

The script will try to guess the location of the Modeller script but it is better to provide the location with the environment variable MODELLEREXEC.

The output from the file is a series of files named model.N.pdb depending on how many models are requested and a list of energies on standard output with the Modeller scores for each file.

Options

-help 

usage information

-loop [chain]inx:sequence[:secstr][=...] 

provide information on which residues to model and optionally provide secondary structure information

-models number 

number of models to be generated

Examples

mutate.pl -seq 10:ADEF 1vii.exp.min.pdb
mutates residues 10 through 13 from VFGM in the original structure to ADEF.

ATOM      1  N   MET     1       3.075  -9.691  -2.062  0.00  0.000         
ATOM      2  CA  MET     1       1.835  -9.001  -2.351  0.00  0.000         
ATOM      3  C   MET     1       0.889  -9.260  -1.188  0.00  0.000         
ATOM      4  O   MET     1       0.838 -10.371  -0.644  0.00  0.000         
ATOM      5  CB  MET     1       1.181  -9.487  -3.654  0.00  0.000         
ATOM      6  CG  MET     1       1.921  -9.123  -4.938  0.00  0.000         
ATOM      7  SD  MET     1       1.107  -9.774  -6.420  0.00  0.000         
ATOM      8  CE  MET     1       0.002  -8.437  -6.776  0.00  0.000         
ATOM      9  N   LEU     2       0.128  -8.242  -0.786  0.00  0.000         
ATOM     10  CA  LEU     2      -0.806  -8.363   0.321  0.00  0.000         

...