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CHANGELOG.md

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RCSB Mol* Changelog

Semantic Versioning

[2.10.6] - 2024-10-28

General

  • Dependency & SCSS updates

[2.10.5] - 2024-10-03

General

  • Dependency updates (e.g., higher resolution on mobile)

[2.10.4] - 2024-09-30

General

  • Dependency updates
  • Sequence Viewer: Adjust visuals of unobserved regions (HELP-21475)

[2.10.3] - 2024-07-01

Bug fixes

  • HELP-21267: don't apply pLDDT coloring to experimental structures

[2.10.2] - 2024-07-01

General

  • Dependency updates

[2.10.1] - 2024-05-22

General

  • Update of RSCC statistics (RO-3983)

[2.10.0] - 2024-05-01

Added

  • GlyGen visuals (RO-4259)

[2.9.4] - 2024-04-16

General

  • Dependency updates

[2.9.3] - 2024-02-28

General

  • Adjust superimpose/motif visuals to include ball-and-stick representation of carbohydrates (RO-4202)

[2.9.2] - 2024-02-26

General

  • Dependency update to Mol* v4

[2.9.1] - 2024-01-24

General

  • Dependency update

[2.9.0] - 2023-12-15

Added

  • Ligand Viewer: expose MP4 export
  • Ligand Viewer: toggle state of controls when expanding viewport

[2.8.3] - 2023-11-06

Added

  • Less intrusive tooltips in ligand viewer (RO-4126)

[2.8.2] - 2023-10-25

Added

  • Option to show density as wireframe (RO-4085)

[2.8.1] - 2023-10-16

Bug fixes

  • Fix undesired interaction between settings panel and the panel on the right

[2.8.0] - 2023-10-02

Added

  • Dedicated ligand viewer for the visualization of CCD/BIRD entries

[2.7.4] - 2023-08-23

Added

  • Motif preset: Show global structure

[2.7.3] - 2023-08-14

Added

  • Relaxed strucmotif distance requirement from 15 to 20 A

[2.7.2] - 2023-07-25

Bug fixes

  • Fix detection of CCD files

[2.7.1] - 2023-06-28

Improvement

  • Delegate the responsibility for setting structure label to representation provider, when available

[2.7.0] - 2023-06-28

Added

  • Allow setting a structure label when loading from URL

[2.6.2] - 2023-06-12

General

  • Update dependencies

Bug fixes

  • Make sure density channels are conditionally hidden (RO-3706)

[2.6.1] - 2023-05-16

General

  • Update dependencies

[2.6.0] - 2023-03-15

Added

  • Upload non-archive structures when searching structure motifs (RO-2771)

Bug fixes

  • Change transformation matrix for alignment example

[2.5.11] - 2023-02-03

Improvement

  • Return trajectory-provider object in loading methods

[2.5.10] - 2023-01-26

Bug fixes

  • Improve handling of collapsed state for assembly symmetry UI

[2.5.9] - 2023-01-03

General

  • Update dependencies
  • Fix handling of struct_oper_ids when extracting structure motifs

[2.5.8] - 2022-10-19

General

  • Bump dependencies to Mol* 3.23.0 (switch to 'auto' mode for EM density maps)

[2.5.7] - 2022-10-07

General

  • Bump dependencies

[2.5.6] - 2022-09-15

Bug fixes

  • Make outgoing strucmotif query URL context-aware

[2.5.5] - 2022-07-28

Bug fixes

  • Strucmotif UI: improve handling of modified & non-standard components

[2.5.4] - 2022-07-28

Bug fixes

  • Avoid deprecated React API
  • Rename 'RCSB PDB Validation Report' to 'Validation Report'

[2.5.3] - 2022-07-24

Bug fixes

  • [Breaking Change] renamed prop-set preset to alignment, renamed representation to colors
  • Pecos related changes

[2.5.2] - 2022-07-21

Bug fixes

  • Fix outgoing strucmotif query URL

[2.5.1] - 2022-07-19

Bug fixes

  • Rename presets/themes for RSCC coloring
  • Improve handling of missing RSCC values

[2.5.0] - 2022-07-18

Added

  • RSCC coloring & validation option

[2.4.2] - 2022-07-08

Bug fixes

  • Strucmotif UI: call blur() to update CSS style properly

[2.4.1] - 2022-05-16

Bug fixes

  • Mol* 3.8.1 (fix Polymer Chain Instance coloring)

[2.4.0] - 2022-05-12

Added

  • Auto-apply pLDDT confidence coloring for single chains

[2.3.0] - 2022-04-04

Added

  • NAKB preset (nucleic acids colored by residue-name, everything else by entity-id)

Bug fixes

  • RO-3186: fix detection of disulfide bridges
  • RO-3194: fix density maps for entries with half-maps

[2.2.1] - 2022-02-28

Bug fixes

  • RO-3063: parse v3 EMDB header XML properly
  • Mol* 3.3.1 (performance improvements)

[2.2.0] - 2022-02-22

Added

  • Expose Quick Styles functionality
  • More fine-grained options for UI controls
  • Expose Canvas3DProps

[2.1.2] - 2022-02-08

General

  • RO-2766: Allow strucmotif of 2 residues

[2.1.1] - 2022-02-07

General

  • Mol* 3.1.0 (Quick Styles panel, default representation tweaks)
  • RO-2968: better error message when density data can't be fetched

[2.1.0] - 2022-02-03

Added

  • Expose GeometryExport functionality

Breaking Internal Change

  • Remove ExportControls et al. in favor of impl from parent project
  • viewer#exportLoadedStructures now returns single structures directly (rather than as a ZIP file)

General

  • Mol* 3.0.2

Bug fixes

  • RO-2605: check for single space-group, hkl, & NCS operator before submitting strucmotif queries

[2.0.9] - 2022-01-24

General

  • Update to Mol* 3.0.0

[2.0.8] - 2022-01-18

General

  • Update Mol* & some other dependencies

[2.0.7] - 2022-01-13

General

  • Update links to new Mol* organization

[2.0.6] - 2022-01-10

Breaking Internal Change

  • Remove PLDDTConfidenceScore in favor of impl from parent project

[2.0.5] - 2022-01-10

General

  • Update Mol* dependency

[2.0.4] - 2022-01-03

General

  • Update Mol* dependency

Bug fixes

  • Show downloaded structures with default/auto representation

[2.0.3] - 2021-12-20

General

  • Hide unusable Animate State Snapshots option

[2.0.2] - 2021-12-16

General

  • Update Mol* dependency

[2.0.1] - 2021-12-07

Bug fixes

  • fix typo in pLDDT behavior name

[2.0.0] - 2021-12-07

Breaking changes

  • loadStructureFromData() is not async anymore
  • Replaced getPlugin() by plugin() getter
  • Signature changes to setFocus(), select(), clearSelection(), and createComponent()
    • Effectively the overloaded methods were replaced by ones that use Target objects to reference residues/ranges
  • Merged Range into Target
    • 'CIF' fields are now represented as camelCase (label_asym_id to labelAsymId)
    • Renamed label_seq_id to labelSeqRange (if referring to a range and not a single residue)
  • ColorProp and PropsetProps now use Target
    • positions and selection props renamed to targets of type Target[]
  • Changed loading methods signature
    • Added optional configuration parameter config?: {props?: PresetProps; matrix?: Mat4; reprProvider?: TrajectoryHierarchyPresetProvider, params?: P}
    • The loading configuration includes an optional trajectory preset provider TrajectoryHierarchyPresetProvider
  • Remove alignMotif methods (& pecos-integration) as the strucmotif service now reports RMSD and transformations for all hits

Bug fixes

  • Support multiple chains in pLDDT confidence coloring

[1.10.1] - 2021-11-30

General

  • Update Mol* dependency

[1.10.0] - 2021-11-22

Added

  • Dedicated UI for quality assessment & validation reports

[1.9.6] - 2021-11-16

General

  • Try to fix packing issues

[1.9.5] - 2021-11-16

General

  • Mol* 2.3.7 (more WebGL fixes)

[1.9.4] - 2021-11-02

General

  • Mol* 2.3.5 and other dependencies (iOS WebGL fixes)

[1.9.3] - 2021-10-18

Bug fixes

  • Rewire index parameter of symmetry preset

[1.9.2] - 2021-10-15

Bug fixes

  • removed implicit 'chain-mode', must be explicitly requested by setting 'extendToChain' to true as part of the part

[1.9.1] - 2021-10-14

Bug fixes

  • More robust 'chain-mode' check in feature preset
  • Don't expand MP4 export controls as part of the symmetry preset

[1.9.0] - 2021-09-29

Added

  • Integrate PDBe/AlphaFold confidence coloring theme

[1.8.8] - 2021-09-28

General

  • Mol* 2.3.1

[1.8.7] - 2021-08-25

General

  • Mol* 2.2.3

[1.8.6] - 2021-08-23

General

  • Display warning if membrane preset calculation fails
  • Add fallback if membrane preset calculation fails

[1.8.5] - 2021-08-11

General

  • Update strucmotif integration with rcsb.org

[1.8.4] - 2021-08-03

General

  • Mol* 2.2.1
  • Reset camera for membrane preset

[1.8.3] - 2021-07-23

General

  • Rename 'Structural Motif Search' to 'Structure Motif Search'

[1.8.2] - 2021-07-20

Bug fixes

  • Post-pare for pecos API changes

[1.8.1] - 2021-07-16

Added

  • Prepare for pecos API changes

[1.8.0] - 2021-07-13

Added

  • Moved code for motif alignment (i.e., talking to pecos) here

[1.7.4] - 2021-07-12

Bug fixes

  • structure selection: handle selection of full chains

[1.7.3] - 2021-07-08

Bug fixes

  • Strucmotif: relative URLs when running inside of sierra

[1.7.2] - 2021-07-05

Bug fixes

  • Code that determines assemblyId is now aware of label_asym_id

[1.7.1] - 2021-07-02

Bug fixes

  • Strucmotif UI now reports chained operators that can be used by sierra/arches/strucmotif
  • Motif preset now works if no assemblyId was provided

Breaking Changes

  • Rename experimental 'structOperExpression' prop to 'struct_oper_id'

[1.7.0] - 2021-06-24

Added

  • Visualize (an arbitrary number of) structural motifs

Bug fixes

  • Fix order of operators in strucmotif queries

[1.6.9] - 2021-06-23

Added

  • Mol* 2.0.7 & some internal cleanup

[1.6.8] - 2021-06-11

Added

  • Hide all but 2Fo-Fc map (RO-2751)

[1.6.6] - 2021-06-08

Added

  • Special density preset with 0(-ish) radius for ligands (RO-2751)

[1.6.5] - 2021-06-03

Bug fixes

  • Access to maps.rcsb.org via HTTPS

[1.6.4] - 2021-06-02

Added

  • Option to show membrane orientation preset

[1.6.3] - 2021-06-01

Bug fixes

  • Improve quality of ANVIL prediction
  • Improve ANVIL & ASA calculation performance

[1.6.2] - 2021-05-12

Bug fixes

  • Clean up viewer init routine

[1.6.1] - 2021-05-04

Bug fixes

  • Multiple region selection (only last one was selected) bug fixed

[1.6.0] - 2021-05-03

Viewer class new methods

  • Added new methods for selection, creating components and focus

[1.5.1] - 2021-04-30

Bug fixes

  • 'Membrane Orientation' preset now honors assembly-ids

[1.5.0] - 2021-04-22

Added

  • feature density preset for ligand validation

Bug fixes

  • hide 'Membrane Orientation' representation from UI

[1.4.2] - 2021-04-20

Bug fixes

  • fix measurement labels
  • hide 'Membrane Orientation' preset from UI

[1.4.1] - 2021-04-06

Bug fixes

  • structure export: getting transformed data

[1.4.0] - 2021-04-02

Added

  • membrane orientation preset by ANVIL

[1.3.5] - 2021-03-25

Bug fixes

  • make sure only structure objects are filtered in for export
  • do not create unit cell object when alignments are loaded

[1.3.4] - 2021-03-25

Bug fixes

  • structure export: getting children for a referenced node correctly

[1.3.3] - 2021-03-24

Bug fixes

  • build

[1.3.2] - 2021-03-24

General

  • major version update of Mol*

[1.3.1] - 2021-03-11

Bug fixes

  • this is a dummy release

[1.3.0] - 2021-03-10

Added

  • expose video export option

[1.2.3] - 2021-03-03

Bug fixes

  • warn when residues are more than 15 A apart (RO-2597)

[1.2.2] - 2021-02-26

Bug fixes

  • switch to 'model' when ligand preset is requested but ligand is not present in assembly '1' - HELP-16678

[1.2.1] - 2021-02-18

Bug fixes

  • limit number of exchanges per position
  • hide State Tree panel

[1.2.0] - 2021-02-16

General

  • structure alignment data visualization

[1.1.0] - 2021-02-08

General

  • structural motif search wizard

[1.0.35] - 2021-02-08

General

  • Mol* 1.3.0

[1.0.34] - 2021-02-05

General

  • bumps dependencies

[1.0.33] - 2021-02-02

General

  • let's call this the initial release