csb-bfite1

Models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions

Overview

usage: csb-bfite [-h] [-c CHAIN] [-s {student,k}] [-a ALIGNMENT] [-o OUTFILE]

: [-n NITER] pdb

Python application for robust structure superposition of an ensemble of structures. bfite models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions.

positional arguments:

pdb: full path to the ensemble

optional arguments:

-h, --help: show this help message and exit

-c CHAIN, --chain CHAIN: Chain (default=A)

-s {student,k}, --scalemixture {student,k}: Scale mixture distribution (default=student)

-a ALIGNMENT, --alignment ALIGNMENT: Alignment in fasta format defining equivalent positions Assumes that chain1 is the first sequence of the alignment and chain2 the second sequence

-o OUTFILE, --outfile OUTFILE: file to which the rotated second structure will be written (default=bfit.pdb)

-n NITER, --niter NITER: Number of optimization steps (default=200)

Releases

Unchanged in 4 releases since Debian 10 (Buster).

10–13