blobs-help.txt

$ gemmi blobs -h
Usage:
 gemmi blobs [options] MTZ_OR_MMCIF PDB_OR_MMCIF

Search for umodelled blobs of electron density.

Options:
  -h, --help            Print usage and exit.
  -V, --version         Print version and exit.
  -v, --verbose         Verbose output.

The area around model is masked to search only unmodelled density.
  --mask-radius=NUMBER  Mask radius (default: 2.0 A).
  --mask-water          Mask water (water is not masked by default).

Searching blobs of density above:
  --sigma=NUMBER        Sigma (RMSD) level (default: 1.0).
  --abs=NUMBER          Absolute level in electrons/A^3.

Blob criteria:
  --min-volume=NUMBER   Minimal volume (default: 10.0 A^3).
  --min-score=NUMBER    Min. this electrons in blob (default: 15.0).
  --min-sigma=NUMBER    Min. peak rmsd (default: 0.0).
  --min-peak=NUMBER     Min. peak density (default: 0.0 el/A^3).

Options for map calculation:
  -d, --diff            Use difference map coefficients.
  --section=NAME        MTZ dataset name or CIF block name.
  -f COLUMN             F column (MTZ label or mmCIF tag).
  -p COLUMN             Phase column (MTZ label or mmCIF tag).
  --weight=COLUMN       (normally not needed) weighting for F.
  -g, --grid=NX,NY,NZ   Minimum grid size.
  --exact               Use the exact grid size specified with --grid.
  -s, --sample=NUMBER   Set spacing to d_min/NUMBER (3 is common).
  -G                    Print size of the grid that would be used and exit.
  --timing              Print calculation times.