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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<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>
+ <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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