MMDS 01. Make/Update PDB File Collection

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • 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 PDB File Collection generates or appends (if exists) a collection that contains n” “PDB protein structures.nn” “If the provided structures are newer a version or new entrant, they are added to the collection.”

MMDS requires an up-to-date collection of protein structure files. the .pdb format is preferred, but will read .mmcif file formats if available. This floe will generate or append (if exists) a collection that contains protein structure files.

New structures, or structures with a newer version that in intput into this floe will be added to the collection.

Related Floes: MMDS 02. Generate Target and Family Dataset, MMDS 03. Structure Prep, MMDS 06. Add structures to MMDS

Computational Cost Scaling Creating a new PDB collection requires significantly more compute resource then if this floe were used to update a preexisting 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: Customer PDB File Collection

Parameter title in user interface (promoted name)

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

Parameter title in user interface (promoted name)

  • Input structure (PDB/MMCIF) files (structure_inp_files) type: file_in: