X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=2bfed88900e97c7c1c04899126e9d1bb56ae1d94;hb=2319ef1a410ce35bf2ef1800fd0be4e779ee44eb;hp=bee83800ed3b864e674571b340fc0957b949793e;hpb=6875edc608179e9710388439099542296f263c15;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html old mode 100755 new mode 100644 index bee8380..2bfed88 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,39 +24,74 @@

- Jalview 2.11.1.3 + Welcome to Jalview Version $$Version-Rel$$ !!

Jalview 2.11.1.3 is the third patch release in the 2.11.1 - series. Critical bugs resolved in this release include:

Find doesn't highlight all motif matches for a sequence.
Mouse over highlighting, CDS reconstruction and problems - with virtual feature popups when working with linked CDS/Protein - alignments.
Result of aligning protein sequences linked to CDS results - in incorrect CDS alignment.
Jalview installer doesn't correctly install Jalview on - paths containing spaces.

19 April 2022

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

- For the full release notes, see the Jalview 2.11.1.3 - release notes. + 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).

- Known Issues + 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:

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. +

+ + +

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

+ 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)