Converting to EMDB-SFF

Converting files to EMDB-SFF

Read the official documentation on how to do this.

Extracting geometry

To perform this, first convert the whole segmentation to EMDB-SFF as outlined above. Next, use the -x/--exclude-geometry and specify the output format as JSON as follows:

# assume you have an HDF5 EMDB-SFF file (.hff)
sff convert --verbose -x geometry.hff -o unannotated.json # or
sff convert --verbose -x geometry.hff --format json

Creating EMDB-SFF files from scratch (Advanced)

You can build EMDB-SFF files from scratch using Python by using the sfftk API. Please read Developing with sfftk-rw for creating EMDB-SFF files from scratch or Developing with sfftk for working with application-specific segmentation file formats.