X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0382f2225f7b83d424b1b6b660b6eef0c7673e3f;hb=33342a9ee15da4873f9fd94bc2330bc73e7bc51f;hp=448430d6afa3682fefa553af124b0750b0df2a49;hpb=448a82c6838c231172078210cfb1bdad138d4604;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 448430d..0382f22 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,70 +24,43 @@
- What's new in Jalview 2.10.0b1 ?
+ What's new in Jalview 2.10.3b1 ?
- Jalview 2.10.0b1 is a patch release for 2.10, the next major release
- in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release
- Notes, but the highlights are below.
+ This release - Jalview 2.10.3b1 is the January 2018 patch release for Version 2.10.3 was released in November 2017. The major focus was to
+ improve Jalview's sequence features datamodel and the scalability of
+ the alignment rendering system. The bugs fixed in this release can be found in the 2.10.3b1
+ Release Notes.
+
+ The highlights for Jalview 2.10.3 include:
- - Drag and drop reinstated for the Jalview desktop on
- Windows, Linux and older OSX systems.
- - Problems loading local PDB files have been fixed
- - Conservation shading can be disabled for PID and consensus
- based colour scheme
+ - Faster and more responsive UI when importing and working
+ with wide alignments and handling hundreds and thousands of
+ sequence features
+ - Improved usability with PDB and UniProt Free Text
+ Search dialog, and new tab for retrieval of sequences for lists of
+ IDs.
+
+ - Short names assigned to sequences retrieved from UniProt
+ - Groovy console upgraded to 2.4.12 (improved support for Java 9)
- Major highlights of the 2.10.0 Release
+
+ Experimental Features
+
+
+ Remember, please enable the Experimental Features option in
+ the Jalview Desktop's Tools menu, and then restart Jalview
+ if you want to try out features below:
+
- - Ensembl sequence fetcher
Annotated
- Genes, transcripts and proteins can be retrieved via Jalview's new
- Ensembl REST
- client. Support for import of Ensembl data allows:
-
- - Aligned locus view
Transcripts
- retrieved for a gene identifier via the Ensembl or
- EnsemblGenomes sequence databases are automatically aligned to
- their reference genome, and introns hidden from the view.
- - Sequence variant data
Jalview
- propagates variant annotation on genomic regions onto
- transcripts and protein products, complete with associated
- metadata such as clinical significance.
-
- - Ensembl and ENA 'show cross-references'
- support
The Calculations menu's 'Show
- cross-references' now offers Ensembl as well as EMBLCDS and
- Uniprot when CDS/Protein mapping data is available for download or
- display. This allows variant annotation to be added directly to an
- alignment of UniProt sequences.
- - Working with structures
-
- - More accurate structure mappings
- Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
- to match structures
- to UniProt sequences, even for structures containing
- multiple copies of a sequence.
- - Import structures as mmCIF
Jalview
- now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large
- structures to be imported, such as the HIV virus capsid
- assembly.
- - Chimera users will need to upgrade to
- 1.11.1
If you use Chimera to view structures
- downloaded by Jalview 2.10, you will need to make sure you are
- running the latest version of Chimera.
-
- - UniProt Free Text Search
The new
- search dialog for UniProt allows you to browse and retrieve
- sequences with free-text search, or structured queries.
- - Reference sequence alignment view
- Jalview 2.9 introduced support for reference sequences. In 2.10,
- when a reference sequence is defined for the alignment, the
- alignment column ruler is now numbered according to the reference
- sequence. The reference sequence for alignment views can also be
- saved and restored from Jalview projects.
+ - Annotation transfer between Chimera and Jalview
Two
+ new entries in
+ the Chimera viewer's Chimera menu allow positional annotation to
+ be exchanged between Chimera and Jalview.
-
+