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ChangeLog.txt
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v1.4.0 (03/12/2019)
- introduced simple semantic versioning according to https://semver.org
v1.3.8.19 (02/12/2019)
- bug fix: xce to read resolution at Mn(I)/sig(I) of 2.0 (and 1.5 if possible) from aimless log; now only reads either one or the other. Datasets table now only shows reso at 2.0 since 1.5 not always shown
- bug fix: read gda barcodes into DB and display in datasets table
v1.3.8.18 (25/11/2019)
- bug fix: added except statement in get_gda_barcodes to catch errors during parsing of multiple visits
v1.3.8.17 (20/11/2019)
- bug fix: refine routine in XChemCootReference.py did not contain argument for covalent bonds
v1.3.8.16 (17/10/2019)
- added CompoundSMILESproduct field in DB to provide SMILES string of product of covalent binders
- new function to use phenix.ligandfit and rhofit to fit ligands into initial maps (all enantiomers are tried and best one is selected)
v1.3.8.15 (15/10/2019)
- new function to define covalent links in XCE COOT interface and to create them with ACEDRG
v1.3.8.14 (14/10/2019)
- new workflow to detect chiral centres in molecules and subsequent enumaration of stereoisomers with phenix.elbow
- selection and modelling of different enantiomers implemented in XCE-COOT interface
v1.3.8.13 (27/09/2019)
- changes to parsing of auto-collected visits ("agamemnon") due to DLS changes to folder structure (now called 'auto' instead of 'agamemnon')
v1.3.8.12 (10/09/2019)
- new task for merging CIF file of non-standard ligand with compoound CIF files
- added exception to catch IOError during opening of gzipped gda logfile
v1.3.8.11 (04/09/2019)
- added few changes to enable parsing of DLS visit directories transfered to other file system
v1.3.8.10 (14/08/2019)
- bug fix: update DB from file system now looks for refine.split.bound-state.pdb instead of refine.bound.pdb
v1.3.8.9 (07/08/2019)
- added option to parse Agamemnon data structure at DLS
- removed obsolete 'Run DIMPLE on All Autoprocessing MTZ files' option from yellow Datasets action box
v1.3.8.8 (25/06/2019)
- path to selected ground-state MTZ/PDB displayed (deposition tab)
- selected PanDDA directoy for ground-state deposition displayed (deposition tab)
- link to group deposition website added to ligand-bound deposition (deposition tab)
- information about ground-state MTZ file added (deposition tab)
v1.3.8.7 (06/06/2019)
- 'model_building' is now the new default initial_model directory
v1.3.8.6 (31/05/2019)
- XChemCOOT-test: added menu funciton to set occupancy of all protein residues to 1 (IMPORTANT: requires COOT v0.8.9.2 or higher)
v1.3.8.5 (29/05/2019)
- bug fix: selection of ground-state mean-map after pandda pre-run: look for average-map instead of mean-map
v1.3.8.4 (23/05/2019)
- bug fix: new initial refinement mechanism does not use the dimple_rerun_on_selected_file subfolder which meant that the .free.mtz file was not selected after the run
- XChemPanDDA export: changed how models will be selected for refinement
- XChemPanDDA export: removed update of obsolete DimplePANDDAhit field in database
- XChemPanDDA export: removed false alarm during export #217
- XChemDeposit: added check for .free.mtz file
- XChemCOOT: add XCE menu (test version only)
- XChemCOOT: add menue item to set occupancy of all protein residues to 1.0 (test version only)
v1.3.8.3 (22/05/2019)
- XChemCOOT: xce-coot messages are now written to xce.log file (not all, yet)
- XChemCOOT: warning message added in case cootOut/Refine_ folder exists
- bug fix: XChemDB: remove hidden characters like \r and \n when updating depositTable
- XChemDB: changed single to double quotation marks (and vice versa) in update depositTable function to allow for example 5' in structure title
v1.3.8.2 (17/05/2019)
- bug fix: avoid overwriting of ligand confidence when updating DN from file system: removed option to 'Update datasource with results from pandda.inspect' + changed XChemPanDDA that only the panddaTable gets only updated for models that ought to be exportet.
- bug fix (temporary): removed label option because it does not behave as expected
- XChemDB: removed PANDDA_site_ligand_placed constraint from query for pandda models
v1.3.8.1 (17/05/2019)
- XCE now ignores empty directories when updating DB from file system
v1.3.8 (25/04/2019)
- added possibility to deposit protein-protein complex structure
- XChemDeposit - create table_1 from final mmcif file
- XChemDeposit - add option to not include event maps in SF mmcif file
- bug fix: XChemDeposit - use beamline information from mainTable
v1.3.7 (18/03/2019)
- implemented pop-up window to remind users where they started xce - minor change
v1.3.6 (14/03/2019)
- new deposition tab with step-by-step instructions regarding PanDDA group depositions
- some obsolete commands were removed from menu and action boxes
- added instructions about how to update DB with PDB codes after group deposition of ligand bound structures
- bug fix: add only structures which are '5-ready for deposition' to tar archive for PDB upload
- increment existing .tar.bz2 files in group_deposition folder before creating a new one
- bug fix: '5-ready for deposition' models can now be added and removed if respective field in COOT interface is triggered
v1.3.5 (07/03/2019)
- added option to use pipedream or phenix.ligand_pipeline for initial refinement (see preferences)
v1.3.4 (01/03/2019)
- bug fix: remove sourcing of pandda setup script in panddaRefine module in case of non-DLS refinement
v1.3.3 (19/02/2019)
- bug fix: wavelength information for apo mmcif file data_template is now also taken from ground-state mtz file
- added additional instructions to deposition tab about ground-state aimless LOG file
- bug fix: removed not supported 'group leader' and 'investigator' option from edit deposition data menu
v1.3.2 (12/02/2019)
- bug fix: removed reference to non-existent labels (prevented opening of