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23 <title>Structure Chooser</title>
28 <strong>Structure Chooser</strong>
32 The Structure Chooser interface allows you to interactively select
33 which PDB structures to view for the currently selected set of
34 sequences. It's opened by selecting the <strong>"3D
35 Structure Data.."</strong> option from the Sequence ID panel's <a
36 href="../menus/popupMenu.html">pop-up menu</a>. The dialog
40 <li>Automatic discovery, retrieval and association of PDB
41 entries for sequences</li>
42 <li>Exploration of meta-data for available 3D structures</li>
43 <li>Automatic selection of the 'best structure' to display for
45 <li>Manual association of PDB entries by entering a PDB Id</li>
46 <li>Association of structure data from a local file (in mmCIF
51 <strong>Automated discovery of structure data</strong>
53 <p>After selecting "3D Structure Data ..", Jalview queries the PDB
54 via the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB ids
55 associated with the sequence. It does this based on the sequence's
56 ID string, and any other associated database IDs.</p>
58 <strong>Exploration of meta-data for available structures</strong>
60 <p>Information on each structure available is displayed in columns
61 in the dialog box. By default, only the title, resolution and PDB
62 identifier are shown, but many more are provided by the PDBe. To
63 configure which ones are displayed, select the 'Configure Displayed
64 Columns' tab and tick the columns which you want to see.</p>
66 <strong>Selection of the best structure for each sequence</strong>
68 <p>Jalview can automatically select the best structures according
69 to meta-data provided by the PDB. By default, the 'Best Quality'
70 structure for each sequence will be selected, but clicking on the
71 drop down menu allows other criteria to be chosen, including
72 Resolution (only defined for X-Ray structures), Highest Protein
73 Chain etc. When 'Invert' is selected, structures are selected in
74 reverse order for the current criteria (e.g. worst quality rather
78 <img src="schooser_main.png" style="width: 464px; height: 369px;">
79 <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
80 <p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
81 <p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
82 <p><img src="schooser_from-file.png" style="width: 468px; height: 370px; ">
83 <p><img src="schooser_cached.png"> -->
84 <br>The screenshot above shows the Structure Chooser interface
85 along with the meta-data of auto-discovered structures for the
86 sample alignment. Note however that if no structures were
87 auto-discovered, a different interface for manual association will
88 be invoked as seen in the screenshot below.
90 <img src="schooser_enter-id.png"
91 style="width: 464px; height: 369px;">
93 <strong>Manual selection/association of PDB files with
96 <p>To manually associate PDB files with a sequence, select 'From
97 File', or 'Enter PDB Id' from the drop-down menu:
99 <li><strong>From File</strong> - allows you to load a PDB file
100 from the local machine or network and associate it with the
101 selected sequence. PDB files associated in this way will also be
102 saved in the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
103 <li><strong>Enter PDB Id</strong> - allows you specify a PDB ID
104 for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
105 to validate and fetch structure data.<br></li>
108 <strong>Viewing existing structures for your sequences</strong>
111 If you have previously associated structure data on the alignment,
112 selecting <strong>Cached PDB Entries</strong> from the drop down
113 menu allows you to select these structures for display.
117 <em>The Structure Chooser interface was introduced in Jalview