X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=2bfed88900e97c7c1c04899126e9d1bb56ae1d94;hb=599ce3ebcced809656e12ca0c0f69abd304f1577;hp=0f0c7f1b747950a5cb60530e7ee2b8fe441182db;hpb=cfcd397b19f70fb39d6d21437db8eb6ffcac3914;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html old mode 100755 new mode 100644 index 0f0c7f1..2bfed88 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,58 +24,74 @@

- Jalview 2.11.1.0 + Welcome to Jalview Version $$Version-Rel$$ !!

19 April 2022

Jalview 2.11.2.2 is the second patch release in the 2.11.2 series.

- Jalview 2.11.1.0 is the first minor release for the 2.11 series. - Along with a number of critical bug fixes and improvements it brings - new functionality for mapping sequence features between CDS and - Protein alignments. It is also the first release made under a new four - number versioning scheme, which will allow us to keep track of - patches and bug fixes. + 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:

Virtual Features
In previous - versions of Jalview, specific nucleotide sequence features such as - genomic variants and exons were transferred to protein products on - import. Jalview 2.11.1 instead provides 'virtual features' that - can be enabled and overlaid on linked CDS/Protein views via their - Sequence - Features dialog. This allows more analyses of nucleotide and - peptide sequence features on alignments in a more flexible and - memory efficient way than in earlier versions.
- Note: Virtual features work best when variants are - annotated with CSQ fields. Please see this - Groovy script workaround if you are working with VCF files - without CSQ fields. -
Improved VCF data import
Standard attributes for - filtering variants (e.g. position, QUAL field etc) are now - extracted from VCF files. This new feature was suggested by a user - at the Jalview booth during ISMB 2019.
Extended feature attributes are exported - in GFF3
Complex attributes from VCF files can be exported - and imported via GFF3
Updated Jalview Installer and Launcher
Jalview's - installation packages are now built with Install4j 8, which brings - better support for Linux and improved control of file - associations. New parameters on the - Jalview launcher allow an upper memory limit to be specified via - a Jalview launch file, to prevent it from hogging your system.
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. +

+ +

- See the 2.11.1.0 - release notes for full details of bugs fixed and new known issues. -

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

- JalviewJS News
With the release of Jalview 2.11.1.0, - the team are now focused on bringing JalviewJS to full production. - To follow our progress take a look at http://www.jalview.org/jalview-js/ - and follow updates on our new JalviewJS - Releases github repository. -

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

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)