MMDS 01. Make/Update RCSB PDB CollectionΒΆ

Category Paths

  • Product-based/SPRUCE

  • Product-based/MMDS

  • Role-based/MMDS Staff User/MMDS Data Prep

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Structural Data Preparation

  • Task-based/Target Prep & Analysis/Protein Preparation


MMDS 01. Make/Update RCSB PDB Collection generates or appends (if exists) a collection that contains PDB protein structures.

Missing structures from the RCSB are downloaded from the RCSB database and added to the collection. Structures are also updated if a newer version of the structures is identified.

AlphaFold structures are also saved in PDB format and updated as new versions are released. These structures can be optionally excluded from the collection.

Parameter title in user interface (promoted name)

  • Collection Name (coll_name) type: string: Name of a new or existing collection for biomolecular source data.For existing collections, an ID can also be used. When supplying a name of an existing collection the latest with that name is updated (if multiple exist).
    Default: RCSB PDB Collection

Parameter title in user interface (promoted name)

  • Output Dataset (data_out) type: dataset_out: Output dataset to write to
    Default: retrieve_failures