Welcome to Jalview Version 2.11.2.2 !!

This is a patch release for the Jalview 2.11.2 series.

This 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 2.11.2.1 release notes.

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