Job: Import 3D Volumes

At a Glance

Import one or more volumes from the filesystem or EMDB.

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. In CryoSPARC v3.3+, you also have the option to download volumes directly from EMDB.

Inputs

This job does not accept any inputs.

Commonly Adjusted Parameters

Volume data path

A valid path referencing one or more volumes on the filesystem. Multiple volumes can be specified using wildcards (*) and other Unix-style pathname patterns.

EMDB ID

A comma-separated list of EMDB identifiers (the 4 or 5 digits following "EMD-").

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 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.

The CryoSPARC master instance must 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/* for this functionality to work.

Type of volume being imported

This job accepts maps, half-maps, sharpened maps, local resolution maps, or masks. All of these volumes are ultimately 3D arrays of voxels, but CryoSPARC imposes limits on which volumes can be plugged into which inputs to avoid, e.g., accidentally trying to refine particles against a binarized mask. Selecting the correct value from this dropdown allows these safeguards to work correctly.

Pixel size (A)

If it is not specified here, the pixel size will be read from the map file header.

Outputs

Imported 3D volume(s) of the appropriate type are produced in separate outputs.

Common Next Steps

Imported mask bases can be thresholded, dilated, and padded with Volume Tools.

Imported maps can be used in a wide variety of jobs, including Homogeneous or Heterogeneous Refinement.

Common Problems

Selecting the incorrect volume type (i.e., map when the volume is actually a mask) will prevent the volume’s use in the desired slot in downstream jobs. Re-importing the volume with the correct type will resolve the issue.