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JAL-4149
Allow low quality structure data to be excluded from a structure viewJAL-4140
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 predictionsJAL-4089
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
structure view saved in project file as zero length entry - project load doesn't open viewer correctlyJAL-3919
fix type on swissmodel structure files so they are re-imported from a Jalview project correctly
Improve selection / control of best covering structures for a sequence
remove defunct RNAView from Jalview
exception when adding additional structures from 3d beacons to existing Jmol view
structure highlight in pymol for amino acid & nucleotide from sequence mouseover
Structure window's viewer-specific menu disappears when many sequences:one chain mappings are presentJAL-3903
Improvements for comparative analysis of repeats in biomolecules
'View using XX' buttons to open selected structures in an available external viewer
Alphafold red/orange/yellow/green colourscheme for structures
'Restore last highlight' to re-show the last highlighted region in a linked alignment window
Faster discovery of available structure data for large numbers of sequences
Jalview always add updated SWISSMODEL models from 3D beacons
"Query 3D Beacons" button / dropdown for structure chooser
colour by->all views doesn't allow colouring same structure from visible regions in different views
don't try to resolve/download SIFTS records for structures not in PDB
Option to insert sequences from structures as additional sequences aligned to their reference sequence in the alignment
Identify canonical Uniprot accessions in protein sequence cross-references
Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
Jalview 3D-Beacons Integration
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