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: [-h] --start START --stop STOP --sequence
                               SEQUENCE [--out_prefix OUT_PREFIX]
                               [--retain_aligned_roots] --pdb PDB [--kic]

Named Arguments

--start Starting resnum. Ex: 24L
--stop Ending resnum. Ex. 42L.
--sequence Sequence of the loop

Any prefix to give results.

Default: “loop_built_


Attempt to keep any aligned root residues during the build

Default: False

--pdb, -s Input model

Run KIC peruturber after closing the loop?

Default: False


Dump midpoint PDBs?

Default: False

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

usage: [-h]

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

usage: [-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

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

usage: [-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