3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>What's new ?</title>
27 <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong>
29 look at the <a href="releases.html#Jalview.$$Version-Rel$$">release
30 notes</a> for this build. Read on for the highlights.
33 <strong>Highlights in 2.11.2</strong>
36 <strong>New features for working with 3D Structure</strong><br />
37 Jalview 2.11.2 features a number of new capabilities:
40 <li><strong>Linked viewing with <em>ChimeraX</em> and
41 <em>PyMol</em></strong><br />Simply configure your prefered viewer for 3D
42 molecular data in <a href="features/preferences.html#structure">Jalview's
43 structure preferences</a>, make sure that Jalview can locate the
44 viewer's installation, and open a new view via the 3D Structure
46 <li><strong>View predicted protein structures via
47 3D-Beacons</strong><br /> Jalview 2.11.2's <a
48 href="features/structurechooser.html">Structure Chooser
49 includes a client for the 3D-Beacons Network</a>, a new service that
50 allows predicted and observed 3D models for proteins in Uniprot
51 from a range of resources, including AlphaFold DB, SWISS-MODEL and
52 a growing number of other resources.</li>
54 <strong>Retrieval of 3D models via 3D-Beacons</strong> <br>The
55 3D-Beacons network (<a
56 href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
57 provides a central point for the retrieval of predicted and
58 observed 3D structures for sequences in Uniprot, including
59 homology models from Swiss-model and deep learning based
60 predictions from the EBI's Alphafold database (Orengo et al. 2020,
61 <a href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
62 See the <a href="features/structurechooser.html">Structure
63 Chooser's documentation</a>.
66 <strong>Support for viewing structures with ChimeraX and
67 Pymol</strong><br> Structures Preferences tab provides new options
68 allowing ChimeraX and Pymol to be used for visualising external 3D
69 structures. Jalview 2.11.2 has been tested with Pymol 2.5.0
70 (community) and 2.5.2 (incentive). For ChimeraX, we recommend
71 using v1.3 or later. Jalview's 3D structure viewer system has been
72 re-architected to allow easier integration of external structure
73 viewers, and takes advantage of the strucViz2 Chimera
74 communications library developed by Scooter Morris (<a
75 href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).
78 For the full release notes, see <a
79 href="releases.html#Jalview.2.11.1.4">the Jalview 2.11.1.4
83 <strong>Known Issues</strong>
85 <p>New known issues in this release affect recovery of
86 CDS/Protein relationships from project files, and interactive
87 selection of protein sequences from a tree built on linked
88 nucleotide sequences. We will provide patches for these issues as