Modelcraft

Added

- Option --mask to provide a custom mask in EM mode instead of using EMDA mapmask

Changed

- Refinement now uses refmacat instead of refmac5

Changed

- Refine input model with and without Sheetbend and choose the best result
- Tests of monomer library entries
- TOXD pipeline test

Changed

- Refmac result to include initial R-work, R-free and FSC values
- Refmac test

Added

- Command line option: --overwrite-directory
- Writing current.cif and current.mtz while running

Added

- New EM pipeline starting from either halfmaps or a single map with optional blurring
- EMDA map mask job
- Servalcat trim, refine, FSC and NE map jobs
- Refmac map to MTZ job
- Libg job (not yet exposed)
- Support for a user-supplied restraints dictionary for ligands
- CCP-EM program tests
- Renaming SUL residues to SO4 and HOH O1 atoms to O on reading a structure

Changed

- Renamed RefmacXray to Refmac
- Flushing print statements so they are written when piping to a file

Removed

- Refmac EM job