0.4.99

• refinement and map calculation related changes
  • "No Refmac" refinement in general
    • vdw exclusion condition revisited
    • mixed derivatives between occupancy and ADPs
    • use obs data resolution
    • set up nonbonded between angle-related atoms when angle is not defined
    • angle restraints: special case for ideal angle of 180 degrees
    • made restraint related keywords common
    • write stats to mmcif
    • print hydrogen related options
  • metals.json
    • cap sigma at 0.02, and factor of 1.5 was needed for mad
  • refmacat
    • now entity_poly is written
• new command: util conf
  • to compare torsion angles between chains or files
• util seq
  • scoring method optimised (hopefully)
• fsc
  • fix bug when using --model and --map together
• fofc
  • hide --omit_proton/--omit_h_electron options, which are experimental and not ready to use
• pdb/mmcif writing
  • mmcif: _atom_site.auth_comp_id was requested
  • pdb: shorten long ccd codes
• switched to nanobind
• requires gemmi 0.7.0

Full Changelog: v0.4.88...v0.4.99

0.4.88

• refmacat: --keep_entities copies entities from input to output
• geometry related changes
  • show sigmas in outliers
  • support symmetry in angles (only through external restraints)
  • ignore hydrogen chem_type from dictionary (not to fail with unknown hydrogen atom types)
  • bug fix: external restraints should be read after loading topology
  • NCS restraint related bug fixes
• included in CCP4 9.0.004
• requires gemmi 0.6.7

Full Changelog: v0.4.82...v0.4.88

0.4.82

• refmacat: bug fix for unrestrained refinement
• refine: bug fix for adp restraint with ncs restraint
• refine_xtal_norefmac
  • experimental implementation of twin refinement
  • in intensity refinement, R1 is calculated instead of "R2", using I/sigma>2
  • fixed broken reading of shelx hkl file
• included in CCP4 9.0.003

Full Changelog: v0.4.77...v0.4.82

0.4.77

• refmacat
  • quick workaround for "given" NCS matrices
  • fix label_seq_id in output mmcif
  • fix erroneous handling of unknown external restraint keywords
  • bug fix for unrestrained refinement
  • write servalcat version to mmcif
• NoRefmac refinement
  • add --newligand_continue option
• refine_xtal_norefmac
  • don't allow negative or more-than-unity occupancies
• fsc
  • made model masking optional (--mask_model)
• included in CCP4 9.0.002

Full Changelog: v0.4.74...v0.4.77

0.4.74

• refmac_keywords: fixed infinite loop occurring when "symm" was specified in an atom spec
• refine/refmacat: add metal links only when requested
• fw: support anomalous intensity input
• included in CCP4 9.0.001

Full Changelog: v0.4.72...v0.4.74

0.4.72

• refinement and map calculation related changes
  • no longer discriminates between ATOM/HETATM records
  • refmacat
    • cap occupancy at 1 for refmac compatibility
    • fix elements in the model using monlib
    • prevent duplicate block names in output mmcif
    • refmac compatibility fix for strict ncs
    • bug fix for missing chain IDs
  • geometry
    • exclude plane atoms within 1-4 distance from vdw
  • refine_spa_norefmac
    • reduced data stats printing
    • new option: --target_bond_rmsz_range
  • refine_spa / refine_spa_norefmac
    • no longer include F(000)
    • lower correlation cutoff for helical symmetry test
    • soft mask creation made much faster
  • "No Refmac" refinement in general
    • now understands refmac keywords "restr tors incl" and excl
    • don't write hydrogen to the output model by default
    • refmac way of weight adjustment
    • write stats json every cycle (for ccp4i2)
    • (experimental) occupancy-only refinement with restraints
    • fixed wrong second derivative calculation wrt occupancy
    • add outliers to stats.json
    • always normalise space group name in the structure
  • refmac keywords:
    • "end" to stop in each file
    • fixed reading "exte weig scal" lines
• new command: util add_op3
• new command: util dnarna
• util geom: add --nucleus option
• requires gemmi 0.6.6
• included in CCP4 9.0.000

0.4.60

• now python -mservalcat works instead of -mservalcat.command_line
• refinement and map calculation related changes
  • group occupancy refinement implemented
  • update old atom names in the model (if available as _chem_comp_atom.alt_atom_id)
  • check duplicated atoms
  • show polymer gaps
  • geometry
    • local NCS restraints implemented
    • nonbonded interaction now doesn't rely on altlocs, but checks sum of occupancies and occupancy group (Refmac way)
    • use all hydrogen torsion angles
    • remove duplicated links
    • fix atom order in bonds: duplication wasn't resolved properly
    • fix link wrongly considered Asu::Different if symmetry code not given in the model file
    • limit ideal angle to [0,180]; e.g. an ideal value of -180 caused a problem
    • fix wrong reporting of torsion angle values
    • ignore bad (NaN) ideal chirals
  • refine_geom --update_dictionary
    • support pdbx_model_Cartn_x_ideal
    • write json file (requested by acedrg)
    • made more robust. there was a risk for H position to be NaN when the geometry was very poor
  • refmacat
    • ignore entities in input
    • refmac workaround for long residue names
    • fix for 3 letter chain IDs
    • fix for Refmac bug (DNA became non-polymer entity after Refmac)
    • don't prepare crd if unrestrained refinement requested
    • fix MAKE keyword reading
    • write H/D expanded mmcif file as well
    • fix issues arisen when used from acedrg: empty chains, wrong date format, space in _entry.id
  • crystallographic refinement
    • refine_xtal_norefmac & refine_cx: fail if model and data symmetry mismatch
    • allow anomalous data input and calculate anomalous difference map
    • remove FP<=0
• util seq: check unknown seq (wrong model)
• util geom: --selection added

requires gemmi 0.6.5.

0.4.39

• refinement and map calculation related changes
  • show bin stats in cycle 0
  • fix ADP constraints
  • harmonic restraints implemented
  • metals: user's keywords have priority
  • refine_xtal_norefmac:
    • intensity: added an FOM proxy
    • solvent mask: use Refmac radii and ignore H/zero-occupancy atoms
    • smoothen ML parameters (D and Sigma)
    • amplitude target and derivatives in C++
  • refmacat
    • add --version option
    • fix buffered output in refmacat
• Refmac pipeline
  • print raw output when failed to check the version #13
• symmetry: bug fix for negative helical rise
• util geom: support exte keywords
• requires gemmi 0.6.3

0.4.32

• refinement and map calculation related changes
  • bug fix: it failed when the link header refers to non existent atoms (including 'gap' links)
  • don't add new links automatically. --no_link_check was obsoleted, and --find_links was added.
  • "no refmac" refinement in general:
    • ADP restraints: don't put distance dependence for bond and angle related pairs.
    • report ADP rms.
    • check -LL difference after ml parameter optimization
    • bug fix in bond angle rmsd reporting
    • bug fix in second derivative smoothing
  • refine_xtal_norefmac:
    • least square scaling significantly improved
    • ADP restraints now uses KL divergence as Refmac does. more controllable parameters
    • automatic weight decision
    • write *_stats.json
    • change --use_all_in_est to --use_work_in_est
    • amplitude target: fixed an anisotropy bug introduced in the previous version
    • intensity: fix wrong derivatives
    • intensity: use all reflection to ML refine B_aniso
    • binning-independent second derivative calculation
    • use previous result as initial for ML scaling and least square scaling
    • guess free flag number automatically
    • ignore nan in CCavg calculation
    • stop extending to lowest resolution
    • bug fix: --ligand didn't work
  • refine_spa_norefmac:
    • fix target function (only affects printed -LL)
    • add --keep_entities
    • bug fix: expand ncs keeping links in Fc calculation
• fsc
  • model based mask and the sharpen-mask-unsharpen procedure are back
• trim
  • fix for symmetry code in the link headers. was problematic when symmetry-related links exist
• fix for numpy/pandas rc* version number
• new command: util adp
  • show ADP stats and histogram
• new command: util seq
  • print sequences of the model and align using input sequence to detect mutations.
• tests fixed for Windows
• included in CCP4 8.0.016

0.4.24

• refinement and map calculation related changes
  • fixed accidental TER problem (TER in between polymer residues caused breakage of polymer links)
  • use of metals.json in restraints MonomerLibrary/monomers#28
  • write SSBOND header in pdb (_struct_conn.conn_type_id disulf in mmcif)
  • support chemcomp block in input model
  • refine_xtal_norefmac:
    • ML parameter refinement stabilised
    • do not load monomer library when --unrestrained
    • report CCavg, the averaged correlation over resolution bins weighted by the number of reflections
    • now --source is required
    • add --no_link_check
    • bug fix and many improvements in intensity target
    • bug fix in space group decision
    • fixed negative diagonal bug in log likelihood part
    • bug fix in same_asu decision in link finding (crystallographic translation was overlooked)
    • add neutron support (but no hydrogen refine)
    • do not overwrite model space group unless needed (as COOT does not seem to support "R -3 m:H" style)
  • refine_spa_norefmac:
    • support symmetry-related links
  • "no refmac" refinement in general:
    • print data stats by resolution
    • add max_vdw_radius to cap van der waals radius as a quick fix for K+
  • per-atom geometry violation score
  • SPA refinement: Fupdate is now calculated as <F> + F_diff
  • refine_geom: --update_dictionary re-adds hydrogen before 2nd round
• refmacat
  • fix vdwr/vand/nonb keyword parsing
  • fix links for DOD when changing to HOH
  • write crd file in output dir
  • delete crd file unless --keep_original_output is given
• fw: find intensity columns automatically and keep test set
• new command: util map2mtz
• CMakeLists.txt added, thanks @wojdyr
• MANIFEST.in added (previous package missed some files for compilation)
• requires gemmi 0.6.2
• included in CCP4 8.0.012