X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=2bfed88900e97c7c1c04899126e9d1bb56ae1d94;hb=599ce3ebcced809656e12ca0c0f69abd304f1577;hp=2944ebd679b935057c6a3091d893dc52762780d9;hpb=6a1a9ecb46fa986460dbe5a85a072f97c96f9121;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html old mode 100755 new mode 100644 index 2944ebd..2bfed88 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,22 +24,74 @@
- Welcome to Jalview Version $$Version-Rel$$ !!
Please take a
- look at the release
- notes for this build.
+ Welcome to Jalview Version $$Version-Rel$$ !!
19 April 2022
+Jalview 2.11.2.2 is the second patch release in the 2.11.2 series.
+- Jalview 2.11.1.5 + 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).
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. It also - addresses an error in the occupancy calculation that occurs when - working with alignments of more than 32,000 sequences.
-- For the full release notes, see the Jalview 2.11.1.5 - release notes. + +
+ 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.
+
+