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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 is 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
50 <strong>Selecting and Viewing Structures</strong>
53 Once one or more structures have been selected, pressing the <strong>View</strong>
54 button will import them into <a
55 href="viewingpdbs.html#afterviewbutton">a new or existing
59 <strong>Automated discovery of structure data</strong>
62 After selecting "3D Structure Data ..", Jalview queries the PDB via
63 the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB IDs
64 associated with the sequence. It does this based on the sequence's
65 ID string, and any other associated database IDs. <br />
68 <strong><a name="cachedstructview">Viewing existing
69 structures for your sequences</a></strong>
72 If you have already loaded 3D structure data for the selected
73 sequences, the structure chooser will first open with the <strong>Cached
74 Structures View</strong>. This view shows associations between each
75 sequence, and chains for 3D structure files already in memory. If
76 you want to download additional structures, select one of the other
77 options from the drop down menu.
80 <strong>Selection of the best structure for each sequence</strong>
82 <p>Jalview can automatically select the best structures according
83 to meta-data provided by the PDB. For alignments with no existing
84 structure data, the 'Best Quality' structure for each sequence will
85 by default be selected, but clicking on the drop down menu allows
86 other criteria to be chosen, including Resolution (only defined for
87 X-Ray structures), Highest Protein Chain etc. When 'Invert' is
88 selected, structures are selected in reverse order for the current
89 criteria (e.g. worst quality rather than best).</p>
92 <img src="schooser_main.png" style="width: 464px; height: 369px;">
93 <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
94 <p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
95 <p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
96 <p><img src="schooser_from-file.png" style="width: 468px; height: 370px; ">
97 <p><img src="schooser_cached.png"> -->
98 <br>The screenshot above shows the Structure Chooser interface
99 along with the meta-data of auto-discovered structures for the
100 sample alignment. If no structures were
101 auto-discovered, options for manually associating PDB records will be shown (see below).
103 <strong>Exploration of meta-data for available structures</strong>
105 <p>Information on each structure available is displayed in columns
106 in the dialog box. By default, only the title, resolution and PDB
107 identifier are shown, but many more are provided by the PDBe. To
108 configure which ones are displayed, select the 'Configure Displayed
109 Columns' tab and tick the columns which you want to see.</p>
111 <img src="schooser_enter-id.png"
112 style="width: 464px; height: 369px;">
114 <strong>Manual selection/association of PDB files with
117 <p>To manually associate PDB files with a sequence, select 'From
118 File', or 'Enter PDB Id' from the drop-down menu:
120 <li><strong>From File</strong> - allows you to load a PDB file
121 from the local machine or network and associate it with the
122 selected sequence. PDB files associated in this way will also be
123 saved in the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
124 <li><strong>Enter PDB Id</strong> - allows you specify a PDB ID
125 for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
126 to validate and fetch structure data.<br></li>
130 <em>The Structure Chooser interface was introduced in Jalview