<em>Add Temperature Factor annotation to alignment</em> - if
selected, values extracted from the Temperature Factor column for
the backbone atoms in the PDB file will be extracted as annotation
- lines shown on the alignment.
+ lines shown on the alignment.<br/><em>Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores.</em>
<p>
- <em>Default structure viewer</em> - choose Jmol or CHIMERA for
+ <em>Default structure viewer</em> - choose Jmol, CHIMERA, CHIMERAX or PYMOL for
viewing 3D structures.
<p>
- <em>Path to Chimera program</em> - Optional, as Jalview will search
- standard installation paths for Windows, Linux or MacOS. If you have
- installed Chimera in a non-standard location, you can specify it
- here, by entering the full path to the Chimera executable program.
- Double-click this field to open a file chooser dialog.
- <p>
+ <em>Path to Chimera/X/Pymol program</em> - Optional, as Jalview will search
+ standard installation paths for Windows, Linux or MacOS. If Jalview cannot locate the installation for your selected structure viewer, a dialog will be shown. If you have
+ installed the chosen viewer in a non-standard location, you can specify it
+ here, by entering the full path to its executable.<br/>For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also <em>double-click this field</em> to open a file chooser dialog.</p>
<p>
<em>PDB Fields shown in Search and Structure Summaries</em> - ticks
in this table indicate fields shown by default when browsing results
</tr>
<tr>
<td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
- <em>22/06/2021</em></strong></td>
- <td align="left" valign="top"><em>Development</em>
+ id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
+ <em>29/09/2021</em></strong></td>
+ <td align="left" valign="top">
+ <ul>
+ <li><!-- --></li>
+ </ul>
+ <em>Development</em>
<ul>
<li>Updated building instructions</li>
</ul></td>
</head>
<body>
<p>
- Welcome to Jalview Version $$Version-Rel$$ !!<br />Please take a
+ <strong>Welcome to Jalview Version $$Version-Rel$$ !!</strong>
+ <br />Please take a
look at the <a href="releases.html#Jalview.$$Version-Rel$$">release
- notes</a> for this build.
+ notes</a> for this build. Read on for the highlights.
</p>
<p>
- <strong>Jalview 2.11.1.4</strong>
+ <strong>Highlights in 2.11.2</strong>
</p>
- <p>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.
+ <p><strong>New features for working with 3D Structure</strong><br/>
+ Jalview 2.11.2 features a number of new capabilities:<ul><li><strong>Linked viewing with <em>ChimeraX</em> and <em>PyMol</em></strong><br/>Simply configure your prefered viewer for 3D molecular data in <a href="features/preferences.html#structure">Jalview's structure preferences</a>, make sure that Jalview can locate the viewer's installation, and open a new view via the 3D Structure Chooser!</li>
+ <li><strong>View predicted protein structures via 3D-Beacons</strong><br/>
+ Jalview 2.11.2's <a href="features/structurechooser.html">Structure Chooser includes a client for the 3D-Beacons Network</a>, 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.
+ </li>
+ <p><strong>Retrieval
</p>
<p>
For the full release notes, see <a
git://source.jalview.org / jalview.git / commitdiff