X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_11_3_0.md;h=7a2c878e7833f1269a3479ebdff20c775a9f2e5c;hb=56a6a69166dc8ea81282c7e69b55930c39787457;hp=7ddd76f38746c25ab29cc5af3748b5c4da460f7a;hpb=bca92e34b044bba83a9e5a0284cd18b4029d0167;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 7ddd76f..7a2c878 100644 --- a/help/markdown/releases/release-2_11_3_0.md +++ b/help/markdown/releases/release-2_11_3_0.md @@ -1,6 +1,6 @@ --- version: 2.11.3.0 -date: 2023-10-03 +date: 2023-10-25 channel: "release" --- @@ -19,6 +19,7 @@ channel: "release" - Visible adjuster marks to grab and adjust annotation panel height and id width - Adjustable ID margin when alignment is wrapped - Command line options and configurable bitmap export preferences for height, width and scale factor +- Show or hide ligands in a Jmol structure view via View Ligands submenu ### Improved support for working with computationally determined models - Alphafold red/orange/yellow/green colourscheme for structures @@ -47,7 +48,7 @@ channel: "release" ### Other improvements - Secondary structure annotation glyphs are rendered anti-aliasing when enabled - Helix and Sheet glyphs vertically centered with respect to grey coil secondary structure annotation track -- Lower line of the sequence group border does not align with vertical and background residue box +- feature should be displayed when its rendering and filtering settings are adjusted - Updated JFreeSVG (https://www.jfree.org/jfreesvg) from 2.1 to 3.4.3 - Name of alignment and view included in overview window's title - "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range @@ -55,6 +56,8 @@ channel: "release" - In Linux desktops' task-managers, the grouped Jalview windows get a generic name - Improved file chooser's 'recent files' view and added filter for 'All known alignment files' - Relative files added to recent files list via import from command line are selected when Jalview opened from same location +- Reduce number of database crossreferences shown in tooltip +- Drag and drop feature colours file on an alignment to quickly apply feature settings - Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button ### Development and Deployment @@ -79,6 +82,7 @@ channel: "release" - reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active - Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser - Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse +- Lower line of the sequence group border does not align with vertical and background residue box - Resizing overview quickly with solid-drags enabled causes exception - Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window - Overview window is saved in project file, and state of 'show hidden regions' is preserved. @@ -88,6 +92,7 @@ channel: "release" - HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2)) ## New Known defects +- 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. - Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled. - Cannot cancel structure view open action once it has been started via the structure chooser dialog - Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately