X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=d849aa21925ef290b1c7de5c335642e49dfa855d;hb=d08dd6439589ba0ed4b683301dffbd19d7d68c79;hp=0cf5661b1143ce17b00aba690d18e3b6a8288807;hpb=214ad7e089fdf9cde66ac5e5d56d498101bbe2c3;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index 0cf5661..d849aa2 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,33 +24,72 @@

- Welcome to Jalview Version $$Version-Rel$$ !! -
Please take a - look at the release + Welcome to Jalview Version $$Version-Rel$$ !!
Please + take a look at the release notes for this build. Read on for the highlights.

Highlights in 2.11.2

New features for working with 3D Structure
- Jalview 2.11.2 features a number of new capabilities:

Linked viewing with ChimeraX and PyMol
Simply configure your prefered 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. -

Retrieval +

+ New features for working with 3D Structure
+ Jalview 2.11.2 features a number of new capabilities described + below.

+
- For the full release notes, see the Jalview 2.11.1.4 - release notes. + 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. 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.
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.
-
New known issues in this release affect recovery of CDS/Protein - relationships from project files, and interactive selection of - protein sequences from a tree built on linked nucleotide sequences. - We will provide patches for these issues as soon as possible.
+
Other highlights include:
+
+
Easier configuration of Jalview's memory + allocation
+
Import of annotated DNA and RNA loci via GenBank and EMBL + style flatfile
+
New command line launcher scripts (.sh, .ps1, .bat) usable on + macOS, Linux/Unix, Windows and documentation in Help +
+ + + + +
+ For the full release notes, see the Jalview 2.11.2.0 + release notes. +
+
+ Known Issues +
+