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Welcome to the Jalview project's issue tracker.
If you experience any problems, please contact James (Jim) Procter.

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  1. Bug JAL-4514
    Residue highlighting in pymol not working in 3.0.4
  2. Bug JAL-4506
    View selection menu under the Jmol views for superimposition not shown
  3. Bug JAL-4486
    secondary structure annotation not mapped correctly to sequence for some structures
  4. Improvement JAL-4484
    Temporarily configure 3d structure viewer via CLI for a jalview session
  5. New Feature JAL-4480
    report proportion of different SSEs / number of distinct SSEs
  6. New Feature JAL-4479
    support import of higher-order complexes and assemblies - "integrative structures"
  7. Improvement JAL-4478
    support import of alphafold3 and multimer prediction metadata
  8. Story JAL-4463
    Importing lots of sequences and structures example
  9. Improvement JAL-4458
    parse PDB / mmCIF header/medata to improve autodetection of models, licensing and cross-references
  10. Improvement JAL-4452
    highlight positions in structures associated with many aligned transcripts
  11. Bug JAL-4440
    Jmol view doesn't show all selected structures in 3d structure chooser mapped to sequences
  12. Bug JAL-4430
    1crn PDB imported as alphafold model, when it is not!
  13. Bug JAL-4416
    Structure view is not shown when loading local structure file for a sequence
  14. Bug JAL-4415
    Enabling just "Add Secondary Structure" Structure preference when importing structure via CLI results in temperature factor being shown in alignment
  15. Task JAL-4411
    Record source metadata in derived/transferred annotation rows
  16. Improvement JAL-4410
    Recognise and map multimeric models from swissmodel via 3d-beacons
  17. Bug JAL-4407
    Secondary structure not available after dragging a 3D structure onto a sequence to associate it
  18. Improvement JAL-4405
    Progress bar and improved speed when associating dropped files with sequences in an alignment
  19. Story JAL-4404
    Explore use of ChimeraX buttonpanel for Jalview<>ChimeraX interoperation
  20. New Feature JAL-4366
    Linked visualisation of Foldseek 3Di MSAs with corresponding 3D structures
  21. Improvement JAL-4350
    Easier to maintain autodiscovery of external structure viewers via exclusion list
  22. Bug JAL-4348
    ChimeraX greater than 1.3/Chimera greater than 1.16.2 are not automatically found even in standard locations
  23. Bug JAL-4344
    --structureimage is only creating a background coloured square image when run through the installer shell script (jalview.sh)
  24. Improvement JAL-4311
    properly handle 3d-beacons sources other than alphafold providing PLDDT confidence scores & shading from model quality score type response
  25. New Feature JAL-4307
    menu options to show or hide HETATM groups in structure view
  26. Bug JAL-4295
    Application hangs when Jalview sends Jmol commands whilst Jmol is acting on commands from Jalview
  27. Bug JAL-4290
    Headless alignment export with structure annotations doesn't include secondary structure and temperature factor
  28. Improvement JAL-4286
    Allow command line / programmatic export of images from external structure viewers
  29. Improvement JAL-4283
    Focus on specific regions of RNA structure when viewing in VARNA
  30. New Feature JAL-4268
    Export commands sent to structure viewers by Jalview to allow customisation
  31. New Feature JAL-4267
    Allow injection of custom structure viewer script when viewing 3D data from Jalview
  32. Epic JAL-4266
    Enable easy customisation of 3D structure views generated by Jalview
  33. Improvement JAL-4265
    Command line option allowing the background colour for a structure view to be configured
  34. New Feature JAL-4254
    Support multichain models with associated PAEs
  35. Improvement JAL-4252
    enable antialiasdisplay in Jmol
  36. New Feature JAL-4244
    Support import of foldseek's m8 alignment files
  37. Improvement JAL-4231
    make it easier to pick preferred experimental modalities for structure data
  38. Bug JAL-4222
    Structure viewer image export can hang when run from command line
  39. Bug JAL-4216
    chains in PDB or mmCIF files with negative RESNUMs for their whole sequence extent throw exceptions
  40. Bug JAL-4208
    Structures imported directly via PDB sequence fetcher have alphafold reliability instead of temperature factor
  41. Improvement JAL-4207
    supress genewise retrieval of ensembl loci when doing 'fetch DB references'
  42. New Feature JAL-4202
    per-structure clipping
  43. New Feature JAL-4197
    view all structures associated with a sequence as an alignment
  44. Task JAL-4196
    fix synchronization issues for structure viewers, tests, and new cli
  45. Bug JAL-4177
    Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
  46. Bug JAL-4176
    jalview queries sifts for locally imported structures
  47. New Feature JAL-4149
    Allow low quality structure data to be excluded from a structure view
  48. Bug JAL-4140
    Temperature and Secondary structure reference annotation not displayed when PDB + PAE loaded via structure chooser local file option
  49. New Feature JAL-4138
    user preferences and structure chooser controls for automatically showing PAE annotation row along side pLDDT when loading structure from alphafold, and control secondary structure and temp factor display
  50. New Feature JAL-4123
    Configure how temperature factor column should be interpreted when loading a 3D structure for a sequence
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