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CSB-HHFRAG(1) User Commands CSB-HHFRAG(1)

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.
November 2017 csb-hhfrag 1.2.5