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23 <title>Annotation from 3D structure data</title>
27 <strong>Working with annotation from 3D structure data</strong>
30 Jalview can process PDB data associated with sequences to display
31 values extracted from the <em>Temperature Factor</em> column for
32 corresponding sites, and secondary structure from DSSP. For computationally determined structures, jalview will show
33 model quality data encoded in the temperature factor column as <em>AlphaFold Reliability</em> (PLDDT) or <em>Model
34 Quality</em> as appropriate.
37 <strong>Extracting data from PDB files<br /></strong>Annotation is
38 created for structure files retrieved directly from the PDB loaded
39 from the file system (via the <strong>Structure→Associate
40 Structure...→From file</strong> option, or when displayed via the View
41 Structures Menu.<br /> Structure annotation is not automatically
42 added to an alignment, but any available structure annotation rows
43 for the current selection or a particular sequence can be added via
44 the <strong>Add Reference Annotation</strong> in the <strong>Selection</strong>
45 and <strong>Sequence ID</strong> sub-menus of the Sequence ID
46 Panel's popup menu.<br /> <em>Please note:</em>Protein structures
47 are analysed <em>in situ</em>.
50 The <a href="../menus/alwannotation.html"><em>Annotations</em>
51 alignment menu</a> provides settings useful for controlling the
52 display of sequence-associated annotation. To compare several tracks from different structures for one or more
53 sequences, use 'sort by label' - which will also display PDB and Chain IDs for secondary structure and temperature
54 factor/quality annotation tracks for easier identification.
57 <strong>Shading sequences by associated structure
59 </strong>The annotation colouring dialog (opened by the <strong>Colour→By
60 Annotation</strong> option) or by right-clicking a particular annotation tracks's label allows sequences with
62 structure data to be shaded according to secondary structure type.
63 Once the dialog is opened, select the <em>Per Sequence</em> option
64 and then choose <em>Secondary structure</em> from the dropdown menu.<br />When
65 colouring alignments by secondary structure, two modes can be
66 employed. The default is to shade sequences with the same colour as
67 the secondary structure glyph. If, however, <em>original
68 colours</em> is selected and another colourscheme has already been
69 applied, then only portions of the sequence with defined secondary
70 structure will be shaded with the previously applied scheme.<br />
73 <strong>Configuration options for processing PDB files<br /></strong>
74 Occasionally, you may wish to disable secondary structure
75 processing. Configuration options in the <strong>Structure</strong>
76 tab in the <strong>Tools→Preferences</strong> dialog allow the
77 processing of structure data to be disabled, or selectively enabled.
78 For more information, take a look at the <a
79 href="preferences.html#structure">documentation for the
83 <em>The display of secondary structure data was introduced in
84 Jalview 2.8.2, and is made possible by Jalview's use of <a
85 href="jmol.html">Jmol's DSSP implementation</a>, based on the
86 original <a href="http://www.ncbi.nlm.nih.gov/pubmed/6667333">Kabsch
87 and Sander algorithm</a> ported by <a
88 href="http://swift.cmbi.ru.nl/gv/dssp/">Robbie P. Joosten
89 and colleagues</a>, and a client for <a
90 href="https://github.com/fjossinet/PyRNA">Fabrice
91 Jossinet's pyRNA services</a> that was developed by Anne Menard, Jim
92 Procter and Yann Ponty as part of the Jalview Summer of Code 2012.