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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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+ * Jalview is free software: you can redistribute it and/or
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+ * of the License, or (at your option) any later version.
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+ * Jalview is distributed in the hope that it will be useful, but
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+ * You should have received a copy of the GNU General Public License
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+<head>
+<title>Annotation from 3D structure data</title>
+</head>
+<body>
+ <p>
+ <strong>Working with annotation from 3D structure data</strong>
+ </p>
+ <p>
+ Jalview can process PDB data associated with sequences to display
+ values extracted from the <em>Temperature Factor</em> column for
+ corresponding sites, and secondary structure from DSSP or RNAView (as
+ appropriate).
+ </p>
+ <p>
+ <strong>Extracting data from PDB files<br /></strong>Annotation is
+ created for structure files retrieved directly from the PDB loaded
+ from the file system (via the <strong>Structure→Associate
+ Structure...→From file</strong> option, or when displayed via the View
+ Structures Menu.<br /> Structure annotation is not automatically
+ added to an alignment, but any available structure annotation rows for
+ the current selection or a particular sequence can be added via the <strong>Add
+ Reference Annotation</strong> in the <strong>Selection</strong> and <strong>Sequence
+ ID</strong> sub-menus of the Sequence ID Panel's popup menu.<br/> <em>Please
+ note:</em>Protein structures are analysed
+ <em>in situ</em>, but Jalview employs a web service to process RNA
+ structures which can cause long delays if your internet connection is
+ slow.
+ </p>
+ <p>
+ The <a href="../menus/alwannotation.html"><em>Annotations</em>
+ alignment menu</a> provides settings useful for controlling the display
+ of secondary structure annotation.
+ </p>
+ <p>
+ <strong>Shading sequences by associated structure annotation<br /></strong>The
+ annotation colouring dialog (opened by the <strong>Colour→By
+ Annotation</strong> option) allows sequences with associated secondary
+ structure data to be shaded according to secondary structure type.
+ Once the dialog is opened, select the <em>Per Sequence</em> option and
+ then choose <em>Secondary structure</em> from the dropdown menu.<br />When
+ colouring alignments by secondary structure, two modes can be
+ employed. The default is to shade sequences with the same colour as
+ the secondary structure glyph. If, however, <em>original colours</em>
+ is selected and another colourscheme has already been applied, then
+ only portions of the sequence with defined secondary structure will be
+ shaded with the previously applied scheme.<br />
+ </p>
+ <p>
+ <strong>Configuration options for processing PDB files<br /></strong>
+ Occasionally, you may wish to disable secondary structure processing.
+ Configuration options in the <strong>Structure</strong> tab in the <strong>Tools→Preferences</strong>
+ dialog allow the processing of structure data to be disabled, or
+ selectively enabled. For more information, take a look at the <a href="preferences.html#structure">documentation for the structure panel</a>.
+ </p>
+ <p>
+ <em>The display of secondary structure data was introduced in
+ Jalview 2.8.2, and is made possible by Jalview's use of <a
+ href="jmol.html">Jmol's DSSP implementation</a>, based on the
+ original <a href="http://www.ncbi.nlm.nih.gov/pubmed/6667333">Kabsch
+ and Sander algorithm</a> ported by <a
+ href="http://swift.cmbi.ru.nl/gv/dssp/">Robbie P. Joosten and
+ colleagues</a>, and a client for <a
+ href="https://github.com/fjossinet/PyRNA">Fabrice Jossinet's
+ pyRNA services</a> that was developed by Anne Menard, Jim Procter and
+ Yann Ponty as part of the Jalview Summer of Code 2012.
+ </em>
+ </p>
+</body>
+</html>
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