Miguel Arbesú -- [email protected]
A script to build mutants from a given PDB file using Pyrosetta. It will replace the existing amino acid at a given position (e.g. 600) with the requested new amino acid in 1-letter code (e.g. "E").
It uses Rossetta's FastRelax and mutate_residue protocols under the hood.
Your will need Rosetta and PyRosetta licenses to use this script. Both suites are free for academic usage. Your can obtain yours here.
For installation, the most straitforward is probably via conda.
- Create a Python environment . Python 3.6-3.9 is supported.
- Follow the instructions
hereto add the pyrosetta channel to your profile (license user and pass required) - Install
pyrosetta.
usage: mutate.py [-h] [--wt_structure WT_STRUCTURE] [--chain CHAIN] [--mutant_position MUTANT_POSITION] [--mutant_aa MUTANT_AA]
[--pack_radius PACK_RADIUS]
optional arguments:
-h, --help show this help message and exit
--wt_structure WT_STRUCTURE
Path to the wild type structure to mutate
--chain CHAIN Chain to mutate. Defaults to A -- the only in AF2 predictions
--mutant_position MUTANT_POSITION
Position to mutate in the canonical sequence
--mutant_aa MUTANT_AA
Amino acid to introduce in 1-letter code
--pack_radius PACK_RADIUS
Radius to determine which neighbor side chains are re-packed
The script is based in the following exammples and documentation pages.
- https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.toolbox.mutants.html#pyrosetta.toolbox.mutants.mutate_residue
- https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb
- https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.02-Working-with-Pose-Residues.ipynb
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