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