X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=f529c568b65f3fade1fd8e4cc0fbe37c83bd3bf6;hb=63747d835b0d6b1e4b3d3d5dd99561af191ee1a9;hp=4b406be513f3538dba99e19b6cec8f3bd8f476ea;hpb=dd193c9ceff22f721c53814fd9c37f269a9edfde;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index 4b406be..f529c56 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,81 +24,66 @@

- Jalview 2.11 - new installer and new capabilities + 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.

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 ej Technologies for providing a free open source project - license for install4j, - and also to Three - Rings Design for Jalview's new over the air update system: Getdown.
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.
Feature filters and attribute colourschemes. A new - Feature Display - Settings dialog allows filters and feature attribute based - colourschemes to be constructed, and a new filters column - added to the Feature - Settings dialog. Jalview's sequence feature datamodel has also - been further optimised, and is now maintained as a separate - library IntervalStoreJ (available at https://github.com/bartongroup/IntervalStoreJ)
Alternative tables for CDS translation. The Translate as cDNA option now - offers alternative amino acid coding schemes.
PCA plots stored in Jalview Projects. The PCA viewer user interface has - also been improved.
Backup files. Jalview will automatically - create backups when overwriting existing files, and - unlike with - earlier versions - should Jalview crash during a save, the original - file will be unaffected. The Backups tab in - Jalview's preferences dialog allows the number and format of - backup filenames to be configured.

- 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, and onwards -

The Jalview application comes bundled with its own independent - Java installation. Version 2.11.0 includes an AdoptOpenJDK Java 1.8 - runtime which will be kept up to date. A Java 11 based installation - is available from the Jalview development pages.

- Saying goodbye...
Long time Jalview users will notice - that this release no longer features the - Vamsas desktop menu, or a Distributed - Annotation System (DAS) tab on the feature settings dialog. - DAS is no longer supported by major bioinformatics databases, and we - decided that it was no longer feasible to maintain either JDAS or - the VAMSAS client library which rely on out-dated Java XML binding - technologies. -

- Next up...
Keep an eye on the Jalview web site for - news about JalviewJS - the web based JavaScript implementation of - Jalview. Whilst Jalview 2.11 has been in development, we have also - been working with Prof. Bob Hanson (Jmol and JSmol) to enable - Jalview to run as both a Java application and a JavaScript app in a - web page. To find out more, open http://www.jalview.org/jalview-js/ - in Chrome or Firefox. -

+ New features for working with 3D Structure
+ Jalview 2.11.2 features a number of new capabilities: + +

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.

+ 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 +