X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2FwhatsNew.html;h=9ee2ab0af982f7eb1daf7f8eb54f21586bcd07e7;hb=3c74b4df923e91c55137dc1b2b5b5ce32775cdb1;hp=b94b9bf3872eb8182e06c968666800fabc483162;hpb=e4a1d321196af18049444db25ce0e2b142cdd984;p=jalview.git diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html index b94b9bf..9ee2ab0 100755 --- a/help/help/html/whatsNew.html +++ b/help/help/html/whatsNew.html @@ -24,31 +24,67 @@

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

- Jalview 2.11.1.4 -

Jalview 2.11.1.4 is the fourth patch release in the 2.11.1 - series. One critical bug was fixed in this release - when Jalview - would occasionally hang when viewing structures in Jmol. This release - also introduces a number of new configuration options for disabling - web service connections used by the Jalview Debian package. -

- For the full release notes, see the Jalview 2.11.1.4 - release notes. + Highlights in 2.11.2

- Known Issues -

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.

+ 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 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 +
+