X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=47fd498a6fe7d2e3350a9e87c526bf1e59d00be5;hp=3ee9b32a21d92f42abb4207696b2c84c893552dd;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 3ee9b32..d1d141d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -23,86 +23,56 @@ What's new ? -

- What's new ? -

-

- Jalview 2.8.2 is the first release produced by our new core - development team.
It incorporates many minor improvements and - bug-fixes, and new features for working with 3D structure data, - shading alignments by secondary structure and generation of alignment - figures as Scalable Vector Graphics.
The majority of - improvements in this version of Jalview concern the desktop - application. As ever, the highlights are detailed below, - and the full list is given in the Jalview 2.8.2 Release Notes. -

-

- Annotation visualisation
The alignment window - includes a new Annotations menu which provides controls for - the layout and display of sequence, group and alignment associated - annotation rows. It also now includes the Autocalculated - Annotation submenu (formerly located in the View menu), which - includes settings for the calculation and display of sequence - consensus, logos, and amino acid conservation for the alignment and - subgroups. -

-

- Sequence associated annotation
New controls - have also been added to the Sequence ID popup menu for the propagation - and display of sequence associated annotation such as secondary - structure assignments and disorder predictions. Annotation associated - with one or a group of sequence already shown on the alignment may be - shown or hidden, and any available annotation from 3D structure or - calculations performed in other Jalview windows can be copied to the - alignment - via the Add Reference Annotation option.
- The Colour by annotation function has also been - improved, allowing secondary structure annotation to be used to shade - sequences and alignment columns. Protein sequences can be coloured - according to the presence of a helix or sheet at each position, and - RNA sequences can be shaded according to each structure's stem/helix - pattern - which enables different RNA folding topologies to be quickly - identified. -

-

- 3D Structural data analysis and display
- Jalview now employs Jmol's PDB data API to retrieve secondary - structure assignments made by the DSSP algorithm. It can also employ - web services to obtain secondary structure assignments from RNA - structures. These assignments are shown as sequence associated - annotation for sequences which have cross-references to the PDB, or - have had PDB files associated with them via the Structures - submenu of the sequence ID popup menu. The extraction and display of - secondary structure and B-factor column annotation is controlled via - a new Structure tab in the Jalview Desktop's - Preferences dialog box. -

-

- Interoperation with UCSF Chimera
The desktop - application can now be configured to employ UCSF Chimera for the - display of 3D structure data. UCSF Chimera is a python-based - high-performance molecular graphics and animation system developed by - the Resource for Biocomputing, Visualisation, and Informatics at the - University of California.
Jalview employs the 'StructureViz' - communication mechanism developed for Cytoscape by Morris et al. - (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism - allows Jalview to send commands to Chimera, enabling structures to be - superimposed and shaded according to associated multiple aligmment - views.
Support for Chimera in Jalview 2.8.2 is experimental, and we - would appreciate feedback ! Please send your comments to - jalview-discuss@jalview.org, and keep up to date with this feature's - development via http://issues.jalview.org/browse/JAL-1333. -

-

- Export of alignment figures as Scalable Vector - Graphics
Scalable Vector Graphics (SVG) files are now widely - supported by web browsers and graphics design programs, and allow - high-quality graphics for interactive exploration and publication. - Jalview now supports the generation of SVGs interactively (via the - Export) menu, and from the command line for server-side figure - generation. -

+

+ What's new in Jalview 2.10.1 ? +

+

+ Jalview 2.10.1 was released on 29th November 2016. Full details are + in the Jalview 2.10.1 + Release Notes, but the highlights are below. This is also the + first release to include contributions from Kira Mourão, who + joined Jalview's core development team in October 2016. +

+ +

+ Warning dialog about updating + your configured URL links
In the desktop prior to Jalview + 2.10.1, the only way to configure custom links for a particular + database cross-reference for a sequence was to give it a name that exactly + matched the database source, and a regular expression for filtering + out any spurious matches generated when the custom linked was tested + against the Sequence's ID string. Since the introduction of the + $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for + database cross-reference accession strings, and if you have custom + links configured, Jalview will raise a warning message so let you + know that you may need to update your links to use $DB_ACCESSION$. +