BioJava can be configured through several properties:

| Property | Description |

| --- | --- |

| `PDB_DIR` | Directory for caching structure files from the PDB. Mirrors the PDB's FTP server directory structure, with `PDB_DIR` equivalent to ftp://ftp.wwpdb.org/pub/pdb/. Default: temp directory |

| `PDB_CACHE_DIR` | Cache directory for other files related to the structure package. Default: temp directory |

These can be set either as java properties or as environmental variables. For example:

Note that your IDE may ignore `.bashrc` settings, but should have a preference for passing VM arguments.