Overview

Basic setup and functionalities

The simplest localpdb setup mode can be obtained by running the following command. This will give access to the lpdb.entries and lpdb.chains dataframes.

Example

localpdb_setup -db_path /path/to/localpdb

In order to sync the protein structures (either in PDB or mmCIF formats), you can rerun localpdb_setup at any time with the following parameters:

Example

localpdb_setup -db_path /path/to/localpdb --fetch_pdb --fetch_cif

You can also install plugins providing additional data with localpdb_setup (also at any time, not necessarily during the initial setup):

Example

localpdb_setup -db_path /path/to/localpdb -plugins Plugin1 Plugin2

The detailed information about the available plugins and their functionalities is available on a separate page.

Finally, you can restore historical localpdb version from the config file as follows:

Example

localpdb_setup -db_path /path/to/localpdb --from_config=backup.tar.gz

Updates

Every week new entries are added to the PDB database, some are removed or modified. To track these changes you can easily update your localpdb database (this'll also update any installed plugins):

Example

localpdb_setup -db_path /path/to/localpdb --update