X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=57aff06e2a3deac2dafc15bca0bc940b506e247c;hb=dd91395fac6acce3696a962e03fb932d1b8c66d5;hp=0cf5661b1143ce17b00aba690d18e3b6a8288807;hpb=214ad7e089fdf9cde66ac5e5d56d498101bbe2c3;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index 0cf5661..57aff06 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 - notes for this build. Read on for the highlights. + Welcome to Jalview Version $$Version-Rel$$ !!

- 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 + This Jalview release 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.

+
- 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. 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.
-
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:
+
+
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 release notes, see the Jalview 2.11.2.0 + release notes. +
+
+ 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)

+