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JAL-4290
Headless alignment export with structure annotations doesn't include secondary structure and temperature factorJAL-4286
Allow command line / programmatic export of images from external structure viewers
Focus on specific regions of RNA structure when viewing in VARNAJAL-4268
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 alignmentJAL-4196
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
Configure how temperature factor column should be interpreted when loading a 3D structure for a sequence
Support import of ESMFold models and confidence predictions
use selected columns for superposition
Interactive highlights of sites on 3D structure corresponding for pAE matrix regions
Exceptions for multiple residue highlights in Jmol
Saving a project to a windows shared drive and loading it again doesn't restore Jmol views
Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
Pymol cannot be opened via Jalview if PymolWin.exe is the configured executable on Windows
Cached PDB structure for FER1_SPIOL in the example project doesn't open in ChimeraX or PyMOL
Cache server queries for 3D structure discovery
FATCAT structure alignment import
annotate sequences with accessible surface area measurements for associated structures
limit database xref discovery to Uniprot when looking up mappings in SIFTS
Consensus secondary structure annotation rows for sequences with multiple sources of structural data
PDB FTS query results in 414 dialog [URL too long]
Mouseover on genomic loci propagated to 2D and 3D structures of transcripts and products
3D Structure chooser fails to select structures from 3D-beacons and pops up a 'null' dialog
Report and visualise overlap between sequence and available structures in structure chooser
Account for visible columns when selecting/filtering available structure data
Allow selections in Pymol to be shown in Jalview
Jalview doesn't associate a structure with all selected sequences with the same name
Need 'Authoritative Identifier' so an import from AlphaFill 3D-beacons yields multiple 'Cached PDB' files
Local 3D structure data files including '%' or ':' in their name cannot be shown in Pymol
Handle biological assemblies shipped via PDBx/mmCIF
Support for multi-character chain IDs
Structure data files with accessions including ':' and '%' are not supported in Pymol
Swissmodel structures including ':' cannot be retrieved and shown on Windows
Highlight region in alignment selected via Jmol
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