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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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