The alphafill executable takes as first argument a program to run. The available programs are:

alphafill create-index

Tool to create a FastA file for the PDB or PDB-REDO structure files

alphafill process

Tool to process an AlphaFold structure

alphafill rebuild-db

Tool to create a database with processed structures, used by the web application

alphafill server

Tool to serve the processed entries as a web application


AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing ligands, cofactors and (metal) ions to the AlphaFold models. By adding the molecular context to these protein structures, the models can be more easily appreciated in terms of function and structural integrity. Consequently, the AlphaFill models can be helpful in designing downstream wet-lab experiments and/or computational studies.

The PDB files used by AlphaFill are normally PDB-REDO files. These files should be located in a directory specified by the --db-dir option. The default for the --pdb-name-pattern option assumes you are using these PDB-REDO files. If you opt to use another source of PDB files, you will have to change the value for this option.

E.g. for regular PDB files, the value should be: ${pdb-dir}/${id:1:2}/${id}.cif.gz

All programs accept at least the following options


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.


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.

See also

alphafill-create-index, alphafill-process, alphafill-rebuild-db, alphafill-process