Welcome to Jalview Version 2.11.2.3 (released 06 July 2022)!!

Jalview 2.11.2.3 is the third patch release in the 2.11.2 series. It addresses a critical bugs affecting Uniprot free text search, users working with very wide alignments and those needing to use alternate JABAWS servers. The tree-viewer now utilises scientific notation for display of very small and large tree lengths, and improvements to the documentation system allow a more streamlined authoring process for release notes.

The 2.11.2 release series provides support for two popular 3D structure visualisation tools, new features for discovery of 3D structures, improved platform integration and a new command line tool allowing Jalview to be more easily called from scripts.

View predicted protein structures via 3D-Beacons
Jalview 2.11.2's Structure Chooser includes a client for the 3D-Beacons Network. Launched in 2021, the 3D-Beacons network (www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/) provides a central point for the retrieval of predicted and observed 3D structures for sequences in Uniprot, including homology models from Swiss-model and deep learning based predictions from the EBI's Alphafold database (Orengo et al. 2020, doi:10.12688/f1000research.20559.1).

Support for viewing structures with ChimeraX and Pymol
Jalview's 3D structure viewer system has been re-architected to allow easier integration of external structure viewers, and takes advantage of the strucViz2 Chimera communications library developed by Scooter Morris (doi:10.1093/bioinformatics/btm329).

The Structures Preferences tab provides new options allowing ChimeraX and Pymol to be used for visualising external 3D structures. Views from all structure viewers are saved in Jalview Projects, allowing them to be shared with others using Jalview 2.11.2 or later, providing they have the same viewer installed and configured to be used with Jalview.

Jalview 2.11.2 has been tested with Pymol 2.5.0 (community) and 2.5.2 (incentive). For ChimeraX, we recommend using v1.3 or later.

Other highlights include:

For the full details, see the Jalview 2.11.2 series release notes.

Known Issues
The following known issues will be addressed in a minor patch release.