Microbial 'omics

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anvi-setup-pdb-database [program]

Setup or update an offline database of representative PDB structures clustered at 95%.

See program help menu or go back to the main page of anvi’o programs and artifacts.

Table of Contents

Can provide


Can consume


Basic usage

This program creates a pdb-db local database that holds PDB structures from this sequence database, which is hosted by the Sali lab. Their database comprises all PDB RCSB sequences that have been clustered at 95% sequence similarity. They seem to update their database every couple of months (thank you guys!).

The purpose of anvi-setup-pdb-database to have a local copy of reference structures that can be used to, for example, get template structures for homology modelling when anvi-gen-structure-database is ran.

Running this program is easy:

anvi-setup-pdb-database --just-do-it

If you already have a pdb-db artifact and are trying to redownload this data, run

anvi-setup-pdb-database --reset

Or if you just want to update your database, run

anvi-setup-pdb-database --update


The output pdb-db database is ~20GB and its contents may take several hours to download.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.