Jalview 2.11.5.0

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Jalview version 2.11.5 is the fifth and (hopefully) final minor release in Jalview’s 2.11 series.

The main highlight for 2.11.5’s release is a new tree visualisation that allows deep exploration of the differences between protein secondary structures derived from distinct sources of 3D structure. This builds on earlier experimental work introduced in Jalview 2.11.4 developed by Renia Correya, the newest member of Jalview’s core developer team. Secondary structure consensus colouring is also possible for alignments and subgroups, allowing divergence to be more easily detected.

The Jalview 2.11.5 command line also has new options making it possible to import, view (and optionally superimpose) several structures associated with one or more sequences in the same structure view.

Several patches are also introduced with this release that address problems reported in 2.11.4.1. These include better support for Jalview running on Windows 11, bugs affecting installations where usernames or directories include characters outside the latin alphabet, and fixes for path issues when launching jalview and saving/restoring Jmol structure views on network drives.

Please note, some of these updates will not automatically apply to existing installations. You will need to update your Jalview installation by visiting https://www.jalview.org/download and downloading the Jalview 2.11.5.0 installer for your platform.

For the full list of new features and patches, please see the release notes below.

This will be the last minor release for the 2.11 series. Please let us know of problems that require urgent patches. All new developments and bug fixes will be targeted to our next major release, Jalview 2.12.

New Features

  • Colour alignments and subgroups by secondary structure conservation
  • Consistent assignment of colours to groups when a tree is cut rather than picking them randomly
  • Display of chain IDs and provider for annotation tracks derived from 3D structure data
  • Sort alignment or selection by sequence description
  • Uniprot Sequence Fetcher dialog allows version numbers to be excluded when given a list of IDs

Secondary structure based trees

  • Create secondary structure annotation trees linked to all chains and structure datasources for one or more sequences
  • Option to show structure providers as coloured lines mapped onto secondary structure annotation trees
  • Annotation tree’s groups are shown as coloured rectangles rather then coloured branch lines
  • Structure import via command line allows multiple structure import and superimposition
  • Annotations associated with selected sequences are also highlighted in annotation panel
  • Extended Jalview’s Alignment Annotation File format to allow key-value pairs and CALC_ID metdata fields to be exported and imported
  • PAE tree is now always shown above the alignment view

Structure and Annotation(s)

  • Model reliability annotations for structures retrieved from 3D-Beacons are labelled with their reported score type (e.g. QMeansDiSCO_)
  • Consensus secondary structure annotation rows for sequences with multiple sources of structural data

Installer

  • Easier OSX installs for people working on enterprise-managed macs via a new ‘Install Jalview.app’ helper tool in the OSX Installation DMG

Command-line

  • Allow many structure(s) to be loaded and viewed (optionally superimposed) via command line
  • Report number of annotation tracks and sequences involved in consensus, conservation, quality, occupancy and secondary structure consensus

Anayltics

  • More robust mechanism for logging usage statistics with jalview.org

Development

  • Improved integration of OSX codesigning process when releasing Jalview

Issues Resolved

  • Sequence ID colourscheme is not applied when view restored from project
  • Jalview can fail to properly import and map a structure to a sequence via the Needleman and Wunsch aligner
  • Jalview 2.11.4.1 doesn’t include full platform details in console output
  • FlatLaF updated from 3.0 to 3.5.4 to fix direct3d related windows 11 redraw problems
  • Location of structure viewer not faithfully saved and restored in project
  • Jmol views cannot be saved in jalview projects on Windows
  • Latest version of ChimeraX not located on Windows
  • Error while using Calculate -> Translate as cDNA
  • New views for a CDS/Protein alignment have an extra ‘cDNA PID’ annotation row
  • Tree node labels are grey when a tree is first created then black when redrawn
  • Jalview freezes when trying to export PNG or EPS from Jmol via the File->Export menu
  • Exported Consensus Annotation when loaded via Load Features/Annotations is interpreted as a Pfam format and appears as sequence onto the alignment
  • Empty row in annotation panel shown when alignment first imported
  • Web URLs that do not provide content or encoding headers are not readable

Command-line

  • Cannot import structure via URL on commandline
  • CLI ignores additional annotation files specified via –annotations
  • Can’t specify URLs via –open=
  • jalview command doesn’t work on Windows when user has a Network homedir

Installer

  • Jalview 2.11.4 installer doesn’t work for usernames that include non-latin characters
  • Getdown sets “com.sun.security.enableAIAcaIssuers”, “true” to ensure intermediate certificates are downloaded if needed
  • Windows installer unusable when Dark Mode is enabled

Development

  • linkCheck task fails for jalview test builds when there are links to whatsNew#experimental in documentation
  • IdWidth display tests failing OSX when scaling=1.0 on a HiDPI display (e.g. 4k monitor)

Known Defects resolved

  • Cannot store/restore group associated secondary structure consensus annotations
  • Sequence ID colourscheme is not applied when view restored from project
  • Cannot view structures imported from a network mount on Windows

New Known Defects

  • Need to select a single sequence before a tree can be calculated for just it’s secondary structure structure annotations
  • Can’t view structures imported by drag and drop of structure URL
  • Secondary structure annotation not mapped correctly to sequence for some structures
  • When jalview is working with large alignments and little memory, Find can fail with a ‘Stack Overflow’ exception
  • Trackpad scrolling on annotation panel when structure view is open causes massive slow down
  • Jmol can fail to map positions for models from some 3D-beacons sources (ongoing issue - partially resolved in 2.11.5.0)
  • Resizing an alignment window from the top can completely obscure sequences and annotation divider
  • Residue highlighting in pymol not working in 3.0.4