pdb-db [artifact]

A DB-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-setup-pdb-database

Required or used by

anvi-gen-structure-database

Description

What is this thing?

This is a comprehensive database of protein structures downloaded from the PDB RSCB that are non-redundant. Currently, it is used for those who want to run anvi-gen-structure-database without an internet connection.

Where does it come from?

A pdb-db can be created via the program anvi-setup-pdb-database. Alternatively, a pdb-db that contains custom structures not found in the RCSB PDB can in theory be generated by the user, but anvi’o currrently offers no reasonable way of doing this.

Notes

The pdb-db generated via anvi-setup-pdb-database is ~20GB.

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