maxit-ccd

A Docker image repository for MAXIT, combining regularly updated wwPDB's resources, in particular PDBx/mmCIF Dictionary and Chemical Component Dictionary (CCD). Using GitHub Actions workflow, the Docker container will be published on every Wednesday (03:10~ UTC) and deployed to the self-hosted servers.

Usage

Pull the container

docker pull ghcr.io/yokochi47/maxit-ccd:main

Check software and resource version information

You can check installed software and resource version information as environment variables.

docker run ghcr.io/yokochi47/maxit-ccd:main env

MAXIT_VER=11.400     # MAXIT version
DDL_VER=2.3.3        # Dictionary Descrition Language (DDL) version
DIC_VER=5.412        # PDBx/mmCIF Dictionary version
CCD_REL=2026-03-21   # Chemical Component Dictionary (CCD) release date 
VAR_REL=2025-09-21   # Amino Acid Protonation Variants Companion Dictionary release date
...

MAXIT command usage

As you know, here's how to use MAXIT:

docker run ghcr.io/yokochi47/maxit-ccd:main maxit

Usage: maxit -input inputfile -output outputfile -o num [ -log logfile ]
  [-o  1: Translate PDB format file to CIF format file]
  [-o  2: Translate CIF format file to PDB format file]
  [-o  8: Translate CIF format file to mmCIF format file]

Run MAXIT command

Next, prepare an arbitrary directory named tmp on the host machine to save the input file(s) input.cif.

.
└── tmp
    └── input.cif

To mount a tmp directory under a predefined working directory mnt on a container machine, use the docker run -v option.

docker run -v ./tmp:/mnt/tmp -u $(id -u):$(id -g) ghcr.io/yokochi47/maxit-ccd:main maxit -input tmp/input.cif -output tmp/output.cif -o 8 -log tmp/maxit.log

Finally, the output files output.cif and maxit.log will be created in the tmp directory. Conguraturations! 🎉

.
└── tmp
    ├── input.cif    
    ├── output.cif
    └── maxit.log

MAXIT's memory leak countermeasures

To ensure a safe conversion, it is recommended to set memory limit (e.g., 16GB, no swap). This will prevent excessive memory usage when converting malformed PDB files.

docker run -v ./tmp:/mnt/tmp -u $(id -u):$(id -g) -m 16g --memory-swap 16g ghcr.io/yokochi47/maxit-ccd:main maxit -input tmp/input.pdb -output tmp/output.cif -o 1 -log tmp/maxit.log

Optional: Build container image

You can build and run the maxit-ccd container image locally.

docker build -t maxit-ccd .
docker run maxit-ccd:latest maxit