- Welcome to Jalview Version $$Version-Rel$$ !!
-
Please take a
- look at the release
+ Welcome to Jalview Version $$Version-Rel$$ !!
Please
+ take a look at the release
notes for this build. Read on for the highlights.
@@ -34,49 +33,54 @@
New features for working with 3D Structure
- Jalview 2.11.2 features a number of new capabilities:
-
+ Jalview 2.11.2 features a number of new capabilities described
+ below.
+
+ 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. 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.
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.
+
Other highlights include:
- 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
- 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. 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.
-
+
For the full release notes, see the Jalview 2.11.2.0 release notes. @@ -85,6 +89,5 @@ Known Issues
-