X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_3_0.md;h=969c53f18d47d6f4e9b36b948e87afe8735b589d;hb=fa35c4093e7b2ff0d572a59b253a3d9f2597bc69;hp=7a2c878e7833f1269a3479ebdff20c775a9f2e5c;hpb=56a6a69166dc8ea81282c7e69b55930c39787457;p=jalview.git

diff --git a/help/markdown/releases/release-2_11_3_0.md b/help/markdown/releases/release-2_11_3_0.md
index 7a2c878..969c53f 100644
--- a/help/markdown/releases/release-2_11_3_0.md
+++ b/help/markdown/releases/release-2_11_3_0.md
@@ -21,7 +21,7 @@ channel: "release"
 - <!-- 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
@@ -33,7 +33,10 @@ channel: "release"
 - <!-- JAL-3858 --> Import and display alphafold alignment uncertainty matrices from JSON
 - <!-- JAL-4134,JAL-4158 --> Column-wise alignment groups and selections and interactive tree viewer for PAE matrices
 - <!-- 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.
@@ -59,6 +62,7 @@ channel: "release"
 - <!-- JAL-4308 --> Reduce number of database crossreferences shown in tooltip
 - <!-- JAL-4315 --> Drag and drop feature colours file on an alignment to quickly apply feature settings
 - <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
+- <!-- JAL-4304,JAL-4305 --> Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly.
 
 ### Development and Deployment
 - <!-- JAL-4054 --> Installers built with install4j10
@@ -81,6 +85,7 @@ channel: "release"
 - <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
 - <!-- JAL-4182 --> reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
 - <!-- JAL-4177 --> Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
+- <!-- JAL-4311 --> 3D beacons sources providing models scored with PLDDT and pTM not sorted against alphaFoldDB models
 - <!-- JAL-4133 --> Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse
 - <!-- JAL-4253 --> Lower line of the sequence group border does not align with vertical and background residue box
 - <!-- JAL-4128 --> Resizing overview quickly with solid-drags enabled causes exception
@@ -90,6 +95,7 @@ channel: "release"
 - <!-- JAL-4255 --> SLF4J produces an error to STDERR at Jalview startup due to missing class
 - <!-- 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
 
 ## 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.
@@ -101,7 +107,7 @@ channel: "release"
 - <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
 - <!-- JAL-3024 --> Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x)
 - <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation
-
+- <!-- JAL-4323 --> scripts adding new fileformats or colourschemes do not work when run via command line