X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=750465f0f41276db62d1e518ed8ad89fd4ec2331;hb=7f9536d5afb5f60359c827be09e97d0f22203130;hp=2e18baead82803c0cd8425b372300b8842e87c10;hpb=05add34141e2161ee8174074de42d56e8afac9b7;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html old mode 100755 new mode 100644 index 2e18bae..750465f --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,62 +24,73 @@

- Jalview 2.11.1.1 + Welcome to Jalview Version $$Version-Rel$$ !!

Jalview 2.11.1.1 is the first patch release for Jalview version - 2.11.1. In addition to fixes for some critical bugs, it also - contains a handful of new features suggested by the Jalview - community.

Jalview 2.11.2.2 is the second patch release in the 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:

Shift+arrow keys navigate to next gap or residue in cursor - mode (enable with F2)
Support import of VCF 4.3 by updating HTSJDK from 2.12 to - 2.23
Improved recognition of GZipped files from local disk or - retrieved via the web
EMBL and EMBL CDS database records retrieved from the - European Nucleotide Archive's Data API as 'EMBL Flatfile' records
Improved Java Console and - logging to help track down problems +
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.
Improved support for Hi-DPI (4K) screens when running on - Linux (Requires Java 11+)

Critical bug fixes include

Jalview runs correctly when launched with Turkish language - settings
Peptide-to-CDS tracking broken when multiple EMBL gene - products shown for a single contig (such as viral genomes)
Errors encountered when processing variants from VCF files - yield "Error processing VCF: Format specifier '%s'" on the console
Count of features not shown can be wrong when there are - both DNA and Protein features mapped to the position under - the cursor
Sequence ID for reference sequence is clipped when Right - align Sequence IDs enabled
Find doesn't report matches that span hidden gapped columns
Jalview ignores file format parameter specifying output - format when exporting an alignment via the command line

+ +

- For the full release notes, see the - Jalview 2.11.1.1 release notes. -

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

- Known Issues -

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

We've had reports from a small number of windows 10 users - who see a warning dialog pop up when Jalview tries to save a new - version of an existing file. If you are affected by this bug and - this latest version of Jalview doesn't fix it, please let us know!
Co-located features exported and re-imported are ordered - differently when shown on alignment and in tooltips. (Also affects - v2.11.1.0)
Drag and drop of alignment file onto alignment window when - in a HiDPI scaled mode in Linux only works for the top left - quadrant of the alignment window
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)