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/>
29 <p>This is a patch release for the Jalview 2.11.2 series.</p>
30 <p>This release series provides support for two popular 3D
31 structure visualisation tools, new features for discovery of 3D
32 structures, improved platform integration and a new command line
33 tool allowing Jalview to be more easily called from scripts.</p>
36 <strong>View predicted protein structures via 3D-Beacons</strong> <br>
37 Jalview 2.11.2's <a href="features/structurechooser.html">Structure
38 Chooser includes a client for the 3D-Beacons Network</a>. Launched in
39 2021, the 3D-Beacons network (<a
40 href="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/">www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/</a>)
41 provides a central point for the retrieval of predicted and observed
42 3D structures for sequences in Uniprot, including homology models
43 from Swiss-model and deep learning based predictions from the EBI's
44 Alphafold database (Orengo et al. 2020, <a
45 href="https://doi.org/10.12688/f1000research.20559.1">doi:10.12688/f1000research.20559.1</a>).<br>
49 <strong>Support for viewing structures with ChimeraX and
50 Pymol</strong><br> Jalview's 3D structure viewer system has been
51 re-architected to allow easier integration of external structure
52 viewers, and takes advantage of the strucViz2 Chimera communications
53 library developed by Scooter Morris (<a
54 href="https://doi.org/10.1093/bioinformatics/btm329">doi:10.1093/bioinformatics/btm329</a>).<br /> <br />
55 The <a href="features/preferences.html#structure">Structures
56 Preferences tab</a> provides new options allowing ChimeraX and
57 Pymol to be used for visualising external 3D structures. Views
58 from all structure viewers are saved in Jalview Projects, allowing
59 them to be shared with others using Jalview 2.11.2 or later,
60 providing they have the same viewer installed and configured to be
61 used with Jalview.<br/><br/>Jalview
62 2.11.2 has been tested with <strong>Pymol 2.5.0 (community)</strong> and <strong>2.5.2
63 (incentive)</strong>. For <strong>ChimeraX, we recommend using v1.3 or later</strong>.
65 <p>Other highlights include:</p>
67 <li>Import of annotated DNA and RNA loci via GenBank and EMBL
69 <li><strong>Easier configuration of <a
70 href="features/preferences.html#startup">Jalview's memory
71 allocation</a></strong></li>
72 <li>Scripts for <a href="features/commandline.html">running
73 Jalview via the command line</a> on macOS, Linux/Unix and Windows.
79 For the full details, see <a
80 href="releases.html#Jalview.2.11.2.1">the Jalview 2.11.2.1
84 <strong>Known Issues</strong> <br />The following known issues will
85 be addressed in a minor patch release.
88 <li>Display of RESNUM sequence features are not suppressed when
89 structures associated with a sequence are viewed with an external
90 viewer (Regression from 2.11.1 series)</li>