Installation

Installing localpdb

The setup of the localpdb is simple and straightforward. Recommended installation way is to use pip (this will also make the localpdb_setup script available in your PATH):

pip install localpdb

The most recent version of localpdb can be installed directly from the repository:

pip install git+https://github.com/labstructbioinf/localpdb.git

Setting up localpdb

Once installed localpdb you need to setup the database in a suitable directory:

localpdb_setup -db_path /path/to/localpdb

Setup script provides additional options if you want to additionally keep the updatable archive of the raw protein structures in various formats or to select the desired PDB mirror:

Option	Description
-db_path PATH	Path to store the localpdb database.
-mirror MIRROR	PDB mirror used to download the raw files. Valid options are: - rcsb (RCSB PDB - US - default), - pdbe (PDBe - UK), - pdbj (PDBj - Japan).
-plugins PLUGINS	Install plugins fetching additional data. More on plugins.
-tmp_path TMP_PATH	Path to store the temporary installation files. Default: /tmp/
--fetch_pdb	Download the protein structures in the PDB format.
--fetch_cif	Download the protein structures in the mmCIF format.
--update	Update localpdb database instead of setting up. More on updates.
--from_config FILE	Setup localpdb from config file. This enables recreation of the historical PDB versions.

Example

Setting up localpdb in directory /ssd/db/localpdb, syncing structures in PDB and mmCIF formats and installing plugins PDBClustering and ECOD:

localpdb_setup -db_path /ssd/db/localpdb --fetch_pdb --fetch_cif -plugins ECOD PDBClustering