---
version: 2.11.3.0
date: 2023-03-07
channel: "release"
---

## New Features
- <!-- JAL-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
- <!-- JAL-4054 --> Installers built with install4j10
- <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
- <!-- JAL-3416 --> FlatLAF default look and feel on Linux, OSX and everywhere else ?

- <!-- JAL-4019 --> Ambiguous Base Colourscheme
- <!-- JAL-4061 --> Find can search sequence features' type and description
- <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
- <!-- JAL-4089 --> Use selected columns for superposition
- <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column

- <!-- 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-4033 --> Selections with visual feedback via contact matrix annotation

- <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
- <!-- JAL-3855 --> Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/

- <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed

- <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.

- <!-- JAL-3119 --> Name of alignment and view included in overview window's title

- <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
- <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type


## Still in progress (delete on release)

- <!-- JAL-2382 --> Import and display sequence-associated contact predictions in CASP-RR format
- <!-- JAL-2349 --> Contact prediction visualisation
- <!-- JAL-2348 --> modularise annotation renderer



## Issues Resolved
- <!-- JAL-3776 --> Cancelling interactive calculation leaves empty progress bar.
- <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
- <!-- JAL-1988 --> Can quit Jalview while 'save project' is in progress
- <!-- JAL-4126 --> 'Use original colours' option of colour by annotation not honoured when restoring view from project
- <!-- JAL-4116 --> PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch)
- <!-- JAL-3784 --> Multiple overview windows can be opened for a particular alignment view when multiple views are present
- <!-- JAL-3785 --> Overview windows opened automatically (due to preferences settings) lack title
- <!-- JAL-2353 --> Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession