CLI Reference

Documentation for the powerfit script.

powerfit --help

usage: powerfit [-h] [--version] [-a <float>] [-nl] [-ncw] [-nr] [-rr <float>]
                [-nt] [-tc <float>] [-c <char>] [-d <dir>] [-n <int>]
                [-g [[<platform>:<device>]]] [-p <int>]
                [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                [--delimiter <str>] [--progressbar | --no-progressbar]
                [--report]
                target resolution template

positional arguments:
  target                Target density map to fit the model in. Data should
                        either be in CCP4 or MRC format
  resolution            Resolution of map in angstrom
  template              Atomic model to be fitted in the density. Format
                        should either be PDB or mmCIF. Valid extensions are
                        .pdb, .ent, .cif, .pdb.gz, .ent.gz, .cif.gz

options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -a <float>, --angle <float>
                        Rotational sampling density in degree. Increasing this
                        number by a factor of 2 results in approximately 8
                        times more rotations sampled. (default: 10)
  -nl, --no-laplace     Do not use the Laplace pre-filter density data.
                        (default: False)
  -ncw, --no-core-weighted
                        Do not use core-weighted local cross-correlation
                        score. (default: False)
  -nr, --no-resampling  Do not resample the density map. (default: False)
  -rr <float>, --resampling-rate <float>
                        Resampling rate compared to Nyquist. (default: 2)
  -nt, --no-trimming    Do not trim the density map. (default: False)
  -tc <float>, --trimming-cutoff <float>
                        Intensity cutoff to which the map will be trimmed.
                        Default is 10 percent of maximum intensity. (default:
                        None)
  -c <char>, --chain <char>
                        The chain IDs of the structure to be fitted. Multiple
                        chains can be selected using a comma separated list,
                        i.e. -c A,B,C. Default is the whole structure.
                        (default: None)
  -d <dir>, --directory <dir>
                        Directory where the results are stored. (default: .)
  -n <int>, --num <int>
                        Number of models written to file. This number will be
                        capped if less solutions are found as requested.
                        (default: 10)
  -g [[<platform>:<device>]], --gpu [[<platform>:<device>]]
                        Off-load the intensive calculations to the GPU.
                        Optionally specify platform and device as
                        <platform>:<device> (e.g., --gpu 0:3). If not
                        specified, uses first device in first platform. If
                        omitted, does not use GPU. (default: None)
  -p <int>, --nproc <int>
                        Number of processors used during search. The number
                        will be capped at the total number of available
                        processors on your machine. (default: 1)
  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set the logging level. (default: INFO)
  --delimiter <str>     Delimiter used in the 'solutions.out' file. For
                        example use ',' or '\t'. Defaults to fixed width.
                        (default: None)
  --progressbar, --no-progressbar
                        Show a progress bar during the search. Disabling the
                        progressbar will improve performance. (default: True)
  --report              Generate a html report with Mol* 3D viewer of the
                        fitted models. (default: False)