Job: Import 3D Volumes

Description

The Import 3D Volumes job type allows you to import one or more 3D volumes, e.g., half-maps, sharpened or unsharpened maps, local resolution maps, and masks. From cryoSPARC v3.3 onwards, you also have the option to download volumes directly from EMDB.

Input

Common Parameters

  • The Volume data path parameter accepts a valid glob (Unix style pathname pattern expansion) as an input, referencing one or more volumes on the filesystem.
  • The EMDB ID parameter accepts a comma-separated list of EMDB identifiers (the 4 or 5 digits following "EMD-").
  • Select Type of volume being imported from the drop-down menu: half-map, sharpened map, local resolution map, or mask.
  • You may wish to specify the Pixel size (A) if known.

Output

  • Imported 3D volume(s)

Importing Volumes from EMDB

If one or more valid EMDB ID is specified, the job will attempt to connect to EMDB servers and download the entry metadata and volume data. The cryoSPARC master instance should allow outbound requests to the EMDB REST API (HTTPS) at https://www.ebi.ac.uk/pdbe/api/emdb/all/* and the EMDB FTP server at ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/* . The JSON metadata associated with the entry will be stored in the job directory and the 3D volume will be stored as a .mrc for downstream processing.

Common Next Steps

  • Homogeneous or heterogeneous refinement, using the imported volume as a starting point for one or more classes respectively
  • Use the imported volume as an input to the Create Templates job for use in the Template Picker.

Example Output

Importing one volume from the file system and two volumes from EMDB.
Importing one volume from the file system and two volumes from EMDB.