Modeller: generate an extended protein conformation from an initial PDB file

The script below takes a pdb file as argument and reads its sequence and topology to generate an extended conformation of the protein. The output file is a pdb file named modeller_out.pdb.

Usage:

./generate_model.py protein.pdb

EDIT: The default behaviour is to generate an extended conformation via the keyword initialize_xyz=True. However, it can be useful to build a native like conformation using the coordinates of the input pdb, for example to repair a buggy pdb file. In that case just call the script as below:

./generate_model.py protein.pdb native