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