- Jalview 2.11.1.5
+ Welcome to Jalview Version $$Version-Rel$$ !!
Jalview 2.11.1.5 is a critical patch release that updates one - of the open source components, log4j, that Jalview relies on. The - update addresses the widely reported log4shell security - vunerability. This release also addresses a bug in the occupancy - calculation that occurs when working with alignments of more than - 32,000 sequences.
+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.
+
- For the full release notes, see the Jalview 2.11.1.5
- release notes.
+ 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.
+
+