Welcome to Jalview Version $$Version-Rel$$ !!
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.