RepairProtein

This repo provides a quick and accurate way to model the missing residues in a .pdb file.
To use this tool, you need to have the original .pdb you want to fix, and the .fasta file for the corresponding sequence from rcsb.org

Environment

Important dependencies:

• modeller 10.4 -> UCSF Modeller license is necessary to use this package. A free academic license is available at https://salilab.org/modeller/registration.html

RUN_RepairProtein.py

Use the RepairProtein class to repair any given .pdb that is in the directory.
This script is contingent on all the target proteins having the same template sequence.

USAGE:

>>>python RUN_RepairProtein.py {OPTIONS}

Required Arguments:
    -i --input_dir: directory where .pdb files of target proteins are found
    -o --output_dir: directory where repaired .pdb files will be added
    -f --fasta: path to .fasta file, which will serve as the template sequence to repair the target proteins

Optional Arguments:
    --tails: if called, will add tail residues to N and C termini.