Modelcraft

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

Fixed

- Catching connection errors when requesting PDB entry contents
- Ensuring MTZ data items use the same ASU definition

Changed

- Comparing per-cycle outputs using R-work instead of R-free

Fixed

- Nautilus test that was looking for a space in a residue name

Fixed

- Trimming spaces from residue names when reading structures

Changed

- Aligned columns in mmCIF output
- CCP4 map setup in EM mode for Gemmi version 0.5.3+

Fixed

- Consecutive residues function to yield last section for known structure IDs