Job: Import 3D Volumes
Last updated
Last updated
Import one or more volumes from the filesystem or EMDB.
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 .
This job does not accept any inputs.
A valid path referencing one or more volumes on the filesystem. Multiple volumes can be specified using wildcards (*) and other Unix-style pathname patterns.
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.
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.
If it is not specified here, the pixel size will be read from the map file header.
Imported 3D volume(s) of the appropriate type are produced in separate outputs.
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.
Imported mask bases can be thresholded, dilated, and padded with .
Imported maps can be used in a wide variety of jobs, including or .