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

# csb-hhfrag(1)

build a dynamic variable-length fragment library for protein structure

## NAME

csb-hhfrag - build a dynamic variable-length fragment library for protein structure

## DESCRIPTION

usage: csb-hhfrag \[-h\] \[-H HHSEARCH\] **-d** DATABASE \[-m MIN\] \[-M MAX\] \[-s STEP\]

-

  \[-c CPU\] \[-g GAP\_FILLING\] \[-F FILTERED\_FILLING\] \[-f\] \[--c-alpha\] \[-t CONFIDENCE\_THRESHOLD\] \[-v VERBOSITY\] \[-o OUTPUT\] QUERY

HHfrag: build a dynamic variable-length fragment library for protein structure prediction with Rosetta AbInitio.

### positional arguments:

- QUERY

  query profile HMM (e.g. created with csb.apps.buildhmm)

### optional arguments:

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

  show this help message and exit

- **-H** HHSEARCH, **--hhsearch** HHSEARCH

  path to the HHsearch executable (default=hhsearch)

- **-d** DATABASE, **--database** DATABASE

  database directory (containing PDBS25.hhm)

- **-m** MIN, **--min** MIN

  minimum query segment length (default=6)

- **-M** MAX, **--max** MAX

  maximum query segment length (default=21)

- **-s** STEP, **--step** STEP

  query segmentation step (default=3)

- **-c** CPU, **--cpu** CPU

  maximum degree of parallelism (default=4)

- **-g** GAP\_FILLING, **--gap-filling** GAP\_FILLING

  path to a fragment file (e.g. CSfrag or Rosetta NNmake), which will be used to complement lowconfidence regions (when specified, a hybrid fragment library be produced)

- **-F** FILTERED\_FILLING, **--filtered-filling** FILTERED\_FILLING

  path to a filtered fragment file (e.g. filtered CSfrag-ments), which will be mixed with the HHfrag-set and then filtered, resulting in a double-filtered library

- **-f**, **--filtered-map**

  make an additional filtered fragment map of centroids and predict torsion angles (default=False)

- **--c-alpha**

  include also C-alpha vectors in the output (default=False)

- **-t** CONFIDENCE\_THRESHOLD, **--confidence-threshold** CONFIDENCE\_THRESHOLD

  confidence threshold for gap filling (default=0.7)

- **-v** VERBOSITY, **--verbosity** VERBOSITY

  verbosity level (default=2)

- **-o** OUTPUT, **--output** OUTPUT

  output directory (default=.)

## AUTHOR

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