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

optional arguments:

show this help message and exit
path to the HHsearch executable (default=hhsearch)
database directory (containing PDBS25.hhm)
minimum query segment length (default=6)
maximum query segment length (default=21)
query segmentation step (default=3)
maximum degree of parallelism (default=4)
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)
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
make an additional filtered fragment map of centroids and predict torsion angles (default=False)
include also C-alpha vectors in the output (default=False)
confidence threshold for gap filling (default=0.7)
verbosity level (default=2)
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