Welcome to Jalview Version $$Version-Rel$$ !!
Please take a look at the release notes for this build. Read on for the highlights.
Highlights in 2.11.2
New features for working with 3D Structure
Jalview 2.11.2 features a number of new capabilities:
Retrieval of 3D models via 3D-Beacons
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).
See the Structure Chooser's documentation.
Support for viewing structures with ChimeraX and
Structures Preferences tab provides new options allowing ChimeraX and Pymol to be used for visualising external 3D structures. 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. 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).
For the full release notes, see the Jalview 126.96.36.199 release notes.
New known issues in this release affect recovery of CDS/Protein relationships from project files, and interactive selection of protein sequences from a tree built on linked nucleotide sequences. We will provide patches for these issues as soon as possible.