- <!-- JAL-4274 --> Command line options and configurable bitmap export preferences for height, width and scale factor
- <!-- JAL-4307 --> Show or hide ligands in a Jmol structure view via View Ligands submenu
-### Improved support for working with computationally determined models
+### Improved support for working with structures and computationally determined models
- <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
- <!-- JAL-4095 --> Interactive picking of low pAE score regions
- <!-- JAL-4027 --> contact matrix datatype in Jalview
- <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
- <!-- JAL-4281 --> Store and restore adjustable ID margin and annotation panel height in Jalview projects
- <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
+- <!-- JAL-4147 --> Per-structure and chain shown when annotation shown sorted by label enabling secondary structure and temperature factor scores from different chains and structures for the same sequence to be visually compared.
+
### Jalview on the command line
- <!-- JAL-4160,JAL-629,JAL-4262,JAL-4265, --> New command line argument framework allowing flexible batch processing, import of structures, pae matrices and other sequence associated data, and alignment and structure figure generation.
- <!-- JAL-4189 --> macOS Dock and KDE taskbar names Jalview icon "java" when running
- <!-- JAL-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
- <!-- JAL-3783 --> Groovy console does not open when Jalview launched from jalview's Java 11 executable jar (available via conda) for recent versions of groovy
+- <!-- JAL-4310 --> Don't offer View model page for sources that do not have model pages
+- <!-- JAL-4298 --> Java Console opening at startup with the exampleFile_v2_7.jvp opening (nearly always) causes Jalview to hang
+- <!-- JAL-4282 --> automatic positioning of ID width for imported project can fail for certain font size configured in User preferences (affects most versions of Jalview prior to 2.11.3.0)
+- <!-- JAL-4223 --> RNAML import missing terminal residue
## New Known defects
- <!-- JAL-4303 --> EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via 'Colour by annotation' unless the alignment's colourscheme has been set to 'None' via the Colours menu.
git://source.jalview.org / jalview.git / blobdiff