X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=e7db2d9cfb46fac9ca6867ec183e226886a83046;hb=782e11934301aff6808365281a3407b65276938f;hp=aaef948117dca8f89c44e32ec52d549612d0cd6f;hpb=e6322a597de6a9d28819a643a598f5e7d60c0242;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index aaef948..e7db2d9 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,46 +24,71 @@

- Jalview 2.11 - major and minor new features + Welcome to Jalview Version $$Version-Rel$$ !!

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.

This is a patch release for the Jalview 2.11.2 series.

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).
+

+ +

+ 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:

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 - based on Three Rings' Getdown system.
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.
PCA plots stored in Jalview Projects
The PCA - viewer has also been enhanced and the user interface revised.
+
Import of annotated DNA and RNA loci via GenBank and EMBL + style flatfile
Easier configuration of Jalview's memory + allocation
Scripts for running + Jalview via the command line on macOS, Linux/Unix and Windows.

+ +

- The full list of bugs fixed in this release can be found in the 2.11 Release Notes. -

+ For the full details, see the Jalview 2.11.2.1 + release notes. +

- Jalview and Java 11, 13, and onwards -

The Jalview application comes bundled with its own independent - Java installation which will be updated automatically from - www.jalview.org. Version 2.11.0 includes an AdoptOpenJDK Java 1.8 - runtime, but installations will be migrated to the latest Java - release once remaining issues have been addressed.

+ Known Issues
The following known issues will + be addressed in a minor patch release. + +

Display of RESNUM sequence features are not suppressed when + structures associated with a sequence are viewed with an external + viewer (Regression from 2.11.1 series)