X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=5ecf2937ae2760b0d61699127430062ff9c14e22;hb=fbc163d1dfc48187b15af561d07b1c62778920d1;hp=3538ff4b1738f95e0516332b803c139306ed7206;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git
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- Jalview 2.11 - major and minor new features
+ Welcome to Jalview Version $$Version-Rel$$ !!
+
Please take a
+ look at the release
+ notes for this build. Read on for the highlights.
- Jalview 2.11 introduces support for loading VCF files, and new
- filters and shading models for sequence features. Under the hood,
- we've addressed many bugs, and also made some important changes in
- the way the Jalview desktop is installed and launched.
-
- - VCF Support. Proteins and genomic contigs with
- chromosomal location annotation (such as protein coding genes
- retrieved from Ensembl) can be annotated with variants imported
- from a local VCF file.
- - The Jalview Launcher and Update System
- Jalview's new installation model means you'll only need to
- download and install Jalview once. After installation, Jalview
- will automatically keep itself up to date. The launcher also sets
- Jalview's memory automatically, so you'll never again have to
- manually configure Java's memory settings.
We are grateful to
- Install4J who provided us with a free license for their
- installation system, and Jalview's over the air update system is
- via Getdown.
-
- The full list of bugs fixed in this release can be found in the 2.11 Release Notes.
+ Highlights in 2.11.2
- Jalview and Java 11, 13, and onwards
-
- Java 11 provides improved performance and better OS
- integration, so we now recommend users select our Java 11 Jalview
- distribution rather than the legacy Java 8 build.
- Known Issues - update for 211
+ New features for working with 3D Structure
+ Jalview 2.11.2 features a number of new capabilities:
+
- - OSX: The 'Open File' dialog for Jalview's Groovy Console
- appears with the title 'Save As', and attempting to select a file
- to load yields a FileNotFound exception.The workaround is to first
- clear the 'Untitled' filename before selecting the file you wish
- to load.
-
- - OSX: Links don't open when clicked on or via the Sequence
- or Alignment window popup menu.
- - OSX (Webstart): Jalview only displays old news feed items
+ - Linked viewing with ChimeraX and
+ PyMol
Simply configure your prefered viewer for 3D
+ molecular data in Jalview's
+ structure preferences, make sure that Jalview can locate the
+ viewer's installation, and open a new view via the 3D Structure
+ Chooser!
+ - View predicted protein structures via
+ 3D-Beacons
Jalview 2.11.2's Structure Chooser
+ includes a client for the 3D-Beacons Network, a new service that
+ allows predicted and observed 3D models for proteins in Uniprot
+ from a range of resources, including AlphaFold DB, SWISS-MODEL and
+ a growing number of other resources.
+ - Easier configuration of Jalview's memory allocation
+
+ 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.
+
+
+ Known Issues
+
+