public.pyrosetta

build_loop_pyrosetta.py

This script builds a loop between two places in a structure with the given sequence, and closes the loop.It is not meant to be the last modeling step, just to create missing density or to prepare for loop modeling.

usage: build_loop_pyrosetta.py [-h] --start START --stop STOP --sequence
                               SEQUENCE [--out_prefix OUT_PREFIX]
                               [--retain_aligned_roots] --pdb PDB [--kic]
                               [--dump_midpoints]

Named Arguments

--start	Starting resnum. Ex: 24L
--stop	Ending resnum. Ex. 42L.
--sequence	Sequence of the loop
--out_prefix	Any prefix to give results. Default: “loop_built_”
--retain_aligned_roots
	Attempt to keep any aligned root residues during the build Default: False
--pdb, -s	Input model
--kic	Run KIC peruturber after closing the loop? Default: False
--dump_midpoints
	Dump midpoint PDBs? Default: False

find_my_glycans.py

This app is the PyRosetta equivalent of GlycanInfo. Print carbohydrate info about the pose. Pass the pose in as an argument

usage: find_my_glycans.py [-h]

find_my_residues.py

Simple app to scan a PDB file and print PDB info and Rosetta understood chains and resnums.

usage: find_my_residues.py [-h] [--chain CHAIN] [--echo_input] pdb_file

Positional Arguments

pdb_file

The PDB file to scan.

Named Arguments

--chain, -c	Specify only a single chain to scan.
--echo_input, -e
	Echo the input structure as output. This is to check how Rosettta worked reading it. Default: False

get_mutation_energy.py

Basic app to get mutation energy of each residue in a particular region using PyRosetta

usage: get_mutation_energy.py [-h] [--pdb PDB] [--outpath OUTPATH]
                              [--filename FILENAME] [--region REGION]
                              [--relax_whole_structure] [--alanine_scan]

Named Arguments

--pdb, -s	Path to PDB file. Required.
--outpath, -o	Full output directory path. Default is pwd/RESULTS Default: “/RESULTS”
--filename, -n	The filename of the results file Default: “mutation_energies.txt”
--region, -r	(region designated as start:end:chain) If none is given, will use whole PDB
--relax_whole_structure, -m
	Relax the whole structure? Default is to only relax chain under question. If no region is set, will default to true Default: False
--alanine_scan, -a
	Trigger the script to do an alanine scan of the mutations instead of a full mutational scan. Default: False