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> <br />Please
28 take a look at the <a href="releases.html#Jalview.$$Version-Rel$$">release
29 notes</a> for this build. Read on for the highlights.
32 <strong>Highlights in 2.11.2</strong>
35 <strong>New features for working with 3D Structure</strong><br />
36 Jalview 2.11.2 features a number of new capabilities described
41 <strong>View predicted protein structures via 3D-Beacons</strong> <br>
42 Jalview 2.11.2's <a href="features/structurechooser.html">Structure
43 Chooser includes a client for the 3D-Beacons Network</a>. Launched in
44 2021, the 3D-Beacons network (<a
45 href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
46 provides a central point for the retrieval of predicted and observed
47 3D structures for sequences in Uniprot, including homology models
48 from Swiss-model and deep learning based predictions from the EBI's
49 Alphafold database (Orengo et al. 2020, <a
50 href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
54 <strong>Support for viewing structures with ChimeraX and
55 Pymol</strong><br> Jalview's 3D structure viewer system has been
56 re-architected to allow easier integration of external structure
57 viewers, and takes advantage of the strucViz2 Chimera communications
58 library developed by Scooter Morris (<a
59 href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).<br /> <br />
60 The <a href="features/preferences.html#structure">Structures
61 Preferences tab</a> provides new options allowing ChimeraX and
62 Pymol to be used for visualising external 3D structures. Jalview
63 2.11.2 has been tested with Pymol 2.5.0 (community) and 2.5.2
64 (incentive). For ChimeraX, we recommend using v1.3 or later.<br />Views
65 from all structure viewers are saved in Jalview Projects, allowing
66 them to be shared with others using Jalview 2.11.2 or later,
67 providing they have the same viewer installed and configured to be
70 <p>Other highlights include:</p>
72 <li><strong>Easier configuration of <a
73 href="features/preferences.html#startup">Jalview's memory
74 allocation</a></strong></li>
75 <li>Import of annotated DNA and RNA loci via GenBank and EMBL
82 For the full release notes, see <a
83 href="releases.html#Jalview.2.11.2.0">the Jalview 2.11.2.0
87 <strong>Known Issues</strong>