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