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JAL-4514
Residue highlighting in pymol not working in 3.0.4
View selection menu under the Jmol views for superimposition not shown
secondary structure annotation not mapped correctly to sequence for some structuresJAL-4484
Temporarily configure 3d structure viewer via CLI for a jalview sessionJAL-4480
report proportion of different SSEs / number of distinct SSEs
support import of higher-order complexes and assemblies - "integrative structures"
support import of alphafold3 and multimer prediction metadataJAL-4463
Importing lots of sequences and structures example
parse PDB / mmCIF header/medata to improve autodetection of models, licensing and cross-references
highlight positions in structures associated with many aligned transcripts
Jmol view doesn't show all selected structures in 3d structure chooser mapped to sequences
1crn PDB imported as alphafold model, when it is not!
Structure view is not shown when loading local structure file for a sequence
Enabling just "Add Secondary Structure" Structure preference when importing structure via CLI results in temperature factor being shown in alignmentJAL-4411
Record source metadata in derived/transferred annotation rows
Recognise and map multimeric models from swissmodel via 3d-beacons
Secondary structure not available after dragging a 3D structure onto a sequence to associate it
Progress bar and improved speed when associating dropped files with sequences in an alignment
Explore use of ChimeraX buttonpanel for Jalview<>ChimeraX interoperation
Linked visualisation of Foldseek 3Di MSAs with corresponding 3D structures
Easier to maintain autodiscovery of external structure viewers via exclusion list
ChimeraX greater than 1.3/Chimera greater than 1.16.2 are not automatically found even in standard locations
--structureimage is only creating a background coloured square image when run through the installer shell script (jalview.sh)
properly handle 3d-beacons sources other than alphafold providing PLDDT confidence scores & shading from model quality score type response
menu options to show or hide HETATM groups in structure view
Application hangs when Jalview sends Jmol commands whilst Jmol is acting on commands from Jalview
Headless alignment export with structure annotations doesn't include secondary structure and temperature factor
Allow command line / programmatic export of images from external structure viewers
Focus on specific regions of RNA structure when viewing in VARNA
Export commands sent to structure viewers by Jalview to allow customisation
Allow injection of custom structure viewer script when viewing 3D data from JalviewJAL-4266
Enable easy customisation of 3D structure views generated by Jalview
Command line option allowing the background colour for a structure view to be configured
Support multichain models with associated PAEs
enable antialiasdisplay in Jmol
Support import of foldseek's m8 alignment files
make it easier to pick preferred experimental modalities for structure data
Structure viewer image export can hang when run from command line
chains in PDB or mmCIF files with negative RESNUMs for their whole sequence extent throw exceptions
Structures imported directly via PDB sequence fetcher have alphafold reliability instead of temperature factor
supress genewise retrieval of ensembl loci when doing 'fetch DB references'
per-structure clipping
view all structures associated with a sequence as an alignment
fix synchronization issues for structure viewers, tests, and new cli
Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
jalview queries sifts for locally imported structures
Allow low quality structure data to be excluded from a structure view
Temperature and Secondary structure reference annotation not displayed when PDB + PAE loaded via structure chooser local file option
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
Configure how temperature factor column should be interpreted when loading a 3D structure for a sequence
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