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23 <title>Structure Chooser</title>
28 <strong>Structure Chooser</strong>
31 The Structure Chooser interface provides a smart technique for
32 selecting PDB structures to view in Jalview by querying readily
33 available meta-data of structures. The Interface can be invoked by
35 <strong>"3D Structure Data.."</strong> option from a sequence's
36 <a href="../menus/popupMenu.html">pop-up menu</a>. Some of the main
37 features it provides are listed below:
39 <li>Automatic discovery, retrieval and association of PDB
40 entries for an alignment's sequences</li>
41 <li>Visualisation of discovered structures' meta-data</li>
42 <li>Ability to configure the meta-data entries to visualise</li>
43 <li>Auto-selection of the best structure via filtering by the
44 available metric parameters in the meta-data (i.e. resolution,
46 <li>Selection of multiple structures in a single operation</li>
48 Additionally, the Structure Chooser retains the following contemporary
51 <li>Manual association of PDB entries via entering the PDB Id
53 <li>Ability to view cached PDB entries</li>
57 <strong>Associating PDB files with Sequences</strong>
58 <br> Discovery/Association of PDB entries to a sequence now
59 happens automatically during the initialisation of the Structure
60 Chooser Interface. Jalview uses the sequence's ID to query the PDB
61 Rest API provided by the EBI to discover PDB Ids associated with the
66 <strong>Configuring displayed meta-data for Structures</strong>
67 <br> To configure the visible meta-data displayed for the
68 discovered structures, click the 'Configure Displayed Columns' tab,
69 then tick the options which you intend to make visible.
73 <strong>Auto-selection of best Structures</strong>
74 <br> Jalview can automatically filter and select the best
75 structures using various metric categories avaialble from the
76 meta-data of the structures. To perform this simply select any of the
77 following options from the drop-down menu in the Structure Chooser
78 interface: Best Uniprot coverage, Higest Resolution, Best Quality,
79 Highest Protein Chain etc. When the 'Invert' option is selected,
80 Jalview returns an inverse result for the current selected option in
84 <img src="schooser_main.png" style="width: 464px; height: 369px;">
85 <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
86 <p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
87 <p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
88 <p><img src="schooser_from-file.png" style="width: 468px; height: 370px; ">
89 <p><img src="schooser_cached.png"> -->
90 <br>The screenshot above shows the Structure Chooser interface
91 along with the meta-data of auto-discovered structures for the
92 sample alignment. Note however that if no structures were
93 auto-discovered, a different interface for manual association will
94 be invoked as seen in the screenshot below.
96 <img src="schooser_enter-id.png"
97 style="width: 464px; height: 369px;"
100 <strong>Manual selection/association of PDB files with
103 <p>To manually associate PDB files with a sequence, select any of
104 the follwing options listed below from the drop-down menu in the
107 <li><strong>From File</strong> - You can load a PDB file from
108 the local machine or network and associate it with the selected
109 sequence. PDB files associated in this way will also be saved in
110 the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
111 <li><strong>Enter PDB Id</strong> - Jalview will use the PDB
112 Rest API, provided by the EBI, to fetch the PDB file with the
114 <li><strong>Cached PDB Entries</strong> - You can view PDB
115 structures which have previously been downloaded/viewed using this
116 option. Jalview caches previously downloaded PDB entries in the
117 computer memory. However, if the project is saved before exiting
118 Jalview, Jalview will serialize the cached entries to the file
123 <em>The Structure Chooser interface was introduced in Jalview