loopModel.pl

Usage

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

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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

loopModel.pl -models 5 -loop 16:STSAASSS 1rnu.pdb
build missing loop for residues 16-23 with the sequence STSAASSS

model 1: -215.72421
model 2: -185.32726
model 3: -197.12695
model 4: -219.20064
model 5: -191.54375

loopModel.pl -models 5 -loop 16:STSAASSS:UUHHHHHU 1rnu.pdb
build missing loop for residues 16-23 with the sequence STSAASSS and a helical secondary structure for residues 18-22

model 1: -235.65416
model 2: -232.83127
model 3: -246.54919
model 4: -251.85773
model 5: -241.54893