X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=6d75f0f4eb718695c72c1a0e79b3003d362d260f;hb=82cba0a99ac7c16b89e8399adb158e6a063fecd3;hp=448430d6afa3682fefa553af124b0750b0df2a49;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 448430d..6d75f0f 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,70 +24,40 @@

- 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 is the January 2018 patch release, which addresses critical bugs including trackpad function in OSX, and display of multiple 3D structures. + The full list bugs fixed in this release can be found in the 2.10.3b1 + Release Notes. In addition, Jalview 2.10.3 provides:

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.

- +