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


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


Display the options allowed for this program.


Display the version of this program.


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


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.


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


Directory containing the alphafilled data


Directory containing the mmCIF files for the PDB


The FastA file containing the PDB sequences


File in CIF format describing the ligands and their modifications.

The default file is af-ligands.cif


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

Default value is 6.


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

Default value is 0.25.


The minimal length of an alignment.

Default value is 85.


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

Default value is 3.5.


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

Default value is 4.


Number of blast hits to use.

Default value is 250.


Blast matrix to use.

Default matrix is BLOSUM62.


Blast word size.

Default value is 3.


Blast expect cut off.

Default value is 10.


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


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


Blast penalty for gap open.

Default value is 11.


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