alphafill-process

Synopsis

alphafill-process [options] <inputfile> [<outputfile>]

Description

alphafill-process is the program to create a new AlphaFill file based on an input model.

--help

Display the options allowed for this program.

--version

Display the version of this program.

--verbose

Use a more verbose output, printing status and progress information.

--quiet

Do not print any status or progress information.

--config configfile

Use the file configfile to collection options. The default is to look for a file called alphafill.conf in the current directory and then in the directory /etc. Use this option to override this and specify your own configuration file.

--pae-file=filename

Specify a specific file containing PAE information, default is to use a filename based on inputfile

--db-dir=dirname

Directory containing the alphafilled data

--pdb-dir=dirname

Directory containing the mmCIF files for the PDB

--pdb-fasta=filename

The FastA file containing the PDB sequences

--ligands=filename

File in CIF format describing the ligands and their modifications.

The default file is af-ligands.cif

--max-ligand-to-backbone-distance=value

The max distance to use to find neighbouring backbone atoms for the ligand in the AF structure.

Default value is 6.

--min-hsp-identity=value

The minimal identity for a high scoring pair (note, value between 0 and 1).

Default value is 0.25.

--min-alignment-length=value

The minimal length of an alignment.

Default value is 85.

--min-separation-distance=value

The centroids of two identical ligands should be at least this far apart to count as separate occurrences.

Default value is 3.5.

--clash-distance-cutoff=value

The max distance between polymer atoms and ligand atoms used in calculating clash scores.

Default value is 4.

--blast-report-limit=value

Number of blast hits to use.

Default value is 250.

--blast-matrix=value

Blast matrix to use.

Default matrix is BLOSUM62.

--blast-word-size=value

Blast word size.

Default value is 3.

--blast-expect=value

Blast expect cut off.

Default value is 10.

--blast-no-filter=value

By default blast will use a low complexity filter. Use this option to turn that off.

--blast-no-gapped

By default blast performs gapped alignment. Use this option to turn that off.

--blast-gap-open

Blast penalty for gap open.

Default value is 11.

--blast-gap-extend=value

Blast penalty for gap extend.

Default value is 1.

--threads=value, -t value

Number of threads to use, zero means all available cores.

Default is to use as many cores as the system has.

See also

alphafill-create-index, alphafill-rebuild-db, alphafill-server, alphafill.conf