csb-hhfrag - build a dynamic variable-length fragment library for
protein structure
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.
- QUERY
- query profile HMM (e.g. created with csb.apps.buildhmm)
- -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=.)
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.