alphafill-server [options] <command>


alphafill-server is the web application server for alphafill. This is a single executable containing everything required to serve AlphaFill as a web service.

Before running the server, you should have created some AlphaFill files using alphafill-process and created a PostgreSQL database with alphafill-rebuild-db.

The command argument must be one of:


Starts a new server process. The program is usually run as a daemon process but for debugging purposes you can run it in the foreground using the --no-daemon,-F flag.

If run in the background, a separate process is forked and will drop privileges while the main process listening to the --port is run using the credentials of the user starting the process. Each connection is passed to child process for handling.

When running in the background, two log files are written to /var/log/alphafill, one called access.log and the other error.log. And a file is written to /var/run/alphafill containing the process ID of the daemon process.


Report the status of a currently running server instance. Result can be either running or stopped.


Stop the currently running server process.


Stops the child process and closes all log files. Then restarts a new child process.

The options for the server are as follows.


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.


Do not fork a background process but run the web server in the foreground.


Address to listen to.

Default value is (i.e. localhost)


Port to listen to.

Default value is 10342


User to run as.

Default value is www-data


Reverse proxy context.

When the server is supposed to be accessible from the outside, you’d best put a reverse proxy server before it since HTTPS is not supported. If you do so, the external address can be provided in this option to generate correct links in the web pages.

Template for links to PDB or PDB-REDO entries. Result pages contain PDB-IDs that have a link. To make them point to something outside the scope of alphafill, you can provide a link template in this option. The variable ${id} will be replaced with the PDB-ID referenced.


The name of the AlphaFill PostgreSQL database.


The owner of the AlphaFill PostgreSQL database.


The password of the AlphaFill PostgreSQL database.


The host of the AlphaFill PostgreSQL database.


The port of the AlphaFill PostgreSQL database.


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.


Template used for locating structure files.

Default value is ${db-dir}/${id:0:2}/AF-${id}-F${chunk}-filled_v${version}.cif.gz


Template used for locating metadata files

Default value is ${db-dir}/${id:0:2}/AF-${id}-F${chunk}-filled_v${version}.cif.json


Template used for locating PDB files

Default value is ${pdb-dir}/${id:1:2}/${id}/${id}_final.cif


The URL of the 3d-beacons service for alphafold

Default value is${id}.json?provider=alphafold


Directory for custom built entries. These are files uploaded by the user of the web service.

Default value is /tmp/alphafill


Location of the yasara executable, needed for optimising.

Default value is /opt/yasara/yasara

See also

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