<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<p><a name="structure"><strong>"Structure"
Preferences tab</strong></a><em> added in Jalview 2.8.2</em></p>
<p><em>Process secondary structure from PDB</em> - if selected, then structure information
-read from PDB will be processed to derive secondary structure annotation.
-<p><em>Use RNAView for secondary structure</em> - if selected, the RNAView service will be
-automatically called to derive secondary structure information.
-<p><em>Add secondary structure annotation to alignment</em> - if selected, PDB secondary structure
-annotation will be shown on the alignment when available.
-<p><em>Add Temperature Factor annotation to alignment</em> - if selected, PDB Temperature Factor
-annotation will be shown on the alignment when available.
+read from PDB will be processed and annotation added to associated sequences.
+<p><em>Use RNAView for secondary structure</em> - if selected, the pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>) will be
+called to derive secondary structure information for RNA chains.
+<p><em>Add secondary structure annotation to alignment</em> - if selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's implementation DSSP</a> will be used to add annotation to polypeptide chains in the structure.
+<p><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.
<p><em>Default structure viewer</em> - choose JMOL or CHIMERA 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><a name="connections"><strong>"Connections"
Preferences tab</strong></a></p>
proxy server and do not enter the settings here.</p>
<p><em>Usage statistics, Questionnaire and Version checks</em><br>
Uncheck these options to prevent Jalview from submitting usage
-statistics to google analytics, checking for jalview questionnaires or
+statistics to google analytics, checking for Jalview questionnaires or
retrieving details of the latest release version (at www.jalview.org).
See the <a href="../privacy.html">user privacy statement</a> for more
information.</p>
EPS files will be a mixture of text and lineart. This produces compact
files that can be edited easily in programs like Microsoft Word and
Adobe Illustrator, but can be problematic if the fonts available to
- jalview are not accessible by the program reading the EPS file.
+ Jalview are not accessible by the program reading the EPS file.
</ul>
<p><em>Automatically set ID width</em><br>
When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.</p>
</pre>
<p>If the boxes are left unchecked for a particular format, the
sequence limits will not be appended to the sequence id.</p>
+<p><em>Embed BioJSON to HTML export</em></p>
+<p>When this option is enabled, Jalview embeds <a href="bioJsonFormat.html">BioJSON</a> data within
+HTML files exported from Jalview at generation time. This enables the exported HTML files
+to be extracted and imported back into the Jalview desktop application at a later time.
+
<p><em>Use Modeller Output</em></p>
<p>This option only applies to PIR format output. Jalview
automatically reads PIR files with sequence descriptions compatible with
git://source.jalview.org / jalview.git / blobdiff