---
name: "csb-bfit"
section: "1"
platform: "linux"
package: "csb"
version: "1.2.5+dfsg-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/csb-bfit"
---

# csb-bfit(1)

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

## NAME

csb-bfit - models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions

## DESCRIPTION

usage: csb-bfit \[-h\] \[-c CHAIN1\] \[-d CHAIN2\] \[-s {student,k}\] \[-a ALIGNMENT\]

-

  \[-o OUTFILE\] \[-n NITER\] \[--em\] pdb1 pdb2

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

### positional arguments:

- pdb1

  full path to the first structure

- pdb2

  full path to the second structure

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-c** CHAIN1, **--chain1** CHAIN1

  Chain of the first structure (default=A)

- **-d** CHAIN2, **--chain2** CHAIN2

  Chain of the second structure (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)

- **--em**

  Use the EM algorithm for optimsation (default=False)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.