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-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Structure Chooser</title>
-</head>
-
-<body>
- <p>
- <strong>Structure Chooser Dialog Box</strong>
- </p>
-
- <p>
- The Structure Chooser allows you to select
- 3D structures to view for the currently selected set of
- sequences. It is opened by selecting the <strong>"3D
- Structure Data..."</strong> option from the Sequence ID panel's <a
- href="../menus/popupMenu.html">pop-up menu</a>. The dialog
- provides:
- </p>
- <ul>
- <li>Automatic discovery, retrieval and association of PDB
- entries for sequences</li>
- <li>Exploration of meta-data for available 3D structures</li>
- <li>Automatic selection of the 'best structure' to display for
- each sequence</li>
- <li>Manual association of PDB entries by entering a PDB Id</li>
- <li>Association of structure data from a local file (in mmCIF
- or PDB format)</li>
- </ul>
- <p>
- <strong>Selecting and Viewing Structures</strong>
- </p>
- <p>The drop-down menu offers different options for structure
- discovery; the 'Cached' view is shown automatically if existing
- structure data has been imported for the selected sequences, and if
- none is available, the import PDB/mmCIF file options are shown.</p>
- <p>
- Once one or more structures have been selected, pressing the <strong>View</strong>
- or <strong>Add</strong> button will import them <a
- href="viewingpdbs.html#afterviewbutton">a new or existing
- structure view</a>. When multiple views are available, use the
- drop-down menu to pick the target viewer for the structures.
- </p>
- <p>
- <strong>Automated discovery of structure data</strong>
- </p>
- <p>
- After selecting "3D Structure Data ..", Jalview queries the PDB via
- the PDBe SOLR Rest API provided by EMBL-EBI to discover PDB IDs
- associated with the sequence. It does this based on the sequence's
- ID string, and any other associated database IDs. <br />
- <br />
- <p>
- <strong><a name="cachedstructview">Viewing existing
- structures for your sequences</a></strong>
- </p>
- <p>
- If you have already loaded 3D structure data for the selected
- sequences, the structure chooser will first open with the <strong>Cached
- Structures View</strong>. This view shows associations between each
- sequence, and chains for 3D structure files already in memory. If
- you want to download additional structures, select one of the other
- options from the drop down menu.
- </p>
- <p>
- <strong>Selection of the best structure for each sequence</strong>
- </p>
- <p>Jalview can automatically select the best structures according
- to meta-data provided by the PDB. For alignments with no existing
- structure data, the 'Best Quality' structure for each sequence will
- by default be selected, but clicking on the drop down menu allows
- other criteria to be chosen, including Resolution (only defined for
- X-Ray structures), Highest Protein Chain etc. When 'Invert' is
- selected, structures are selected in reverse order for the current
- criteria (e.g. worst quality rather than best).</p>
- <p>
-
- <img src="schooser_main.png" style="width: 499px; height: 437px;">
- <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
- <p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
- <p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
- <p><img src="schooser_from-file.png" style="width: 468px; height: 370px; ">
- <p><img src="schooser_cached.png"> -->
- <br>The screenshot above shows the Structure Chooser displayed after
- selecting all the sequences in the Jalview example project. If no
- structures were auto-discovered, options for manually associating
- PDB records will be shown (see below).<p>
- <strong>Exploration of meta-data for available structures</strong>
- </p>
- <p>Information on each structure available is displayed in columns
- in the dialog box. By default, only the title, resolution and PDB
- identifier are shown, but many more are provided by the PDBe. To
- configure which ones are displayed, select the 'Configure Displayed
- Columns' tab and tick the columns which you want to see.</p>
- <p>
- <img src="schooser_enter-id.png"
- style="width: 464px; height: 173px;">
- <br/>
- <strong>Manual selection/association of PDB files with
- Sequences</strong>
- </p>
- <p>To manually associate PDB files with a sequence, select 'From
- File', or 'Enter PDB Id' from the drop-down menu:
- <ul>
- <li><strong>From File</strong> - allows you to load a PDB file
- from the local machine or network and associate it with the
- selected sequence. PDB files associated in this way will also be
- saved in the <a href="jalarchive.html">Jalview Archive file</a>.<br></li>
- <li><strong>Enter PDB Id</strong> - allows you specify a PDB ID
- for your sequence. The PDB Rest API, provided by EMBL-EBI, is used
- to validate and fetch structure data.<br></li>
- </ul>
-
- <p>
- <em>The Structure Chooser interface was introduced in Jalview
- 2.9. </em>
- </p>
-</body>
-</html>
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