X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=9ee2ab0af982f7eb1daf7f8eb54f21586bcd07e7;hb=3c74b4df923e91c55137dc1b2b5b5ce32775cdb1;hp=a448aaa174103c5bab74fefb0f557ba61f3165e5;hpb=6ac89f1f1acdd697eb27d1b0e776c7cde0563002;p=jalview.git
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- Jalview 2.11.1.3
+ Welcome to Jalview Version $$Version-Rel$$ !!
+
Please take a
+ look at the release
+ notes for this build. Read on for the highlights.
- Jalview 2.11.1.3 is the third patch release, fixing a bug
- introduced in last weeks Jalview 2.11.1.1 release affecting display
- of Jalview's example project for some users. Together, these
- releases include fixes for a number of critical bugs, and also contains a
- handful of new features suggested by the Jalview community.
-
- - 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
-
- - 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.
+ Highlights in 2.11.2
- Known Issues
-
+ New features for working with 3D Structure
+ Jalview 2.11.2 features a number of new capabilities:
+
- - 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
+ - Linked viewing with ChimeraX and
+ PyMol
Simply configure your preferred viewer for 3D
+ molecular data in Jalview's
+ structure preferences, make sure that Jalview can locate the
+ viewer's installation, and open a new view via the 3D Structure
+ Chooser!
+ - View predicted protein structures via
+ 3D-Beacons
Jalview 2.11.2's Structure Chooser
+ includes a client for the 3D-Beacons Network, a new service that
+ allows predicted and observed 3D models for proteins in Uniprot
+ from a range of resources, including AlphaFold DB, SWISS-MODEL and
+ a growing number of other resources.
+ - Easier configuration of Jalview's memory allocation
+
+ Retrieval of 3D models via 3D-Beacons
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).
+ See the Structure
+ Chooser's documentation.
+
+
+ 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. 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.
+
+
+ For the full release notes, see the Jalview 2.11.2.0
+ release notes.
+
+
+ Known Issues
+
+