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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
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- * Jalview is free software: you can redistribute it and/or
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- * of the License, or (at your option) any later version.
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- * Jalview is distributed in the hope that it will be useful, but
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- * 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>PDB Viewing</title>
-</head>
-<body>
- <p>
- <strong>Discovering and Viewing PDB Structures</strong>
- </p>
- Jalview can be used to explore the 3D structures of sequences in an
- alignment by following the steps below:
- <ol>
- <li>Select the <strong>"3D Structure Data..."</strong> option
- from a sequence's <a href="../menus/popupMenu.html">pop-up
- menu</a> to open the <a href="structurechooser.html">Structure
- Chooser</a> dialog box.
- <ul>
- <li>If one or more structures exists for the given
- sequence, the <a href="structurechooser.html">Structure
- Chooser</a> dialog will open with them listed in the results
- pane.
- </li>
- <li>However, if no structure was found, the <a
- href="structurechooser.html">Structure Chooser</a> interface
- will present options for manual association of PDB structures.
- </li>
- </ul>
- </li>
- <li><strong>Selecting Structures</strong><br />You can select
- the structures that you want to open and view by selecting them
- with the mouse and keyboard.<br />By default, if structures were
- discovered, then some will already be selected according to the
- criteria shown in the drop-down menu. The default criteria is
- 'highest resolution', simply choose another to pick structures in
- a different way.<br />
- <ul>
- <li><strong>Viewing Cached Structures</strong><br />If
- previously downloaded structures are available for your
- sequences, the structure chooser will automatically offer them
- via the <strong>Cached Structures</strong> view. If you wish
- to download new structures, select one of the PDBe selection
- criteria from the drop-down menu.</li>
- </ul></li>
- <li><strong>To view selected structures, click the <strong>"View"</strong>
- button.
- </strong><br />
- <ul>
- <li>Additional structure data will be downloaded with the
- EMBL-EBI's dbfetch service</li>
- <li><a href="siftsmapping.html">SIFTS</a> records will also
- be downloaded for mapping UniProt protein sequence data to PDB
- coordinates.</li>
- <li>A new structure viewer will open, or you will be
- prompted to add structures to existing viewers (see <a
- href="#afterviewbutton">below</a> for details).
- </li>
- </ul></li>
- </ol>
- <p>
- <strong>Structure Viewers in the Jalview Desktop</strong><br /> The
- <a href="jmol.html">Jmol viewer</a> has been included since Jalview
- 2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
- provided it is installed and can be launched by Jalview. The default
- viewer can be configured in the <a href="preferences.html#structure">Structure
- tab</a> in the <strong>Tools→Preferences</strong> dialog box.
-
- <p>
- Structure data imported into Jalview can also be processed to
- display secondary structure and temperature factor annotation. See
- the <a href="xsspannotation.html">Annotation from Structure</a> page
- for more information.
- </p>
- <p>
- <img src="schooser_viewbutton.png"
- style="width: 465px; height: 81px" /><br/> <strong><a
- name="afterviewbutton">Controlling where the new structures
- will be shown</a></strong>
- <br />The Structure Chooser offers several options
- for viewing a structure. <br/><strong>New View</strong> will open a new
- structure viewer for the selected structures, but if there are views
- already open, you can select which one to use, and press the <strong>Add</strong>
- button. Jalview can automatically superimpose new structures based
- on the linked alignments - but if this is not desirable, simple
- un-tick the <strong>Superpose Structures</strong> checkbox.
-
- </p>
- <p>
- <em>Superposing structures</em><br/>Jalview superposes structures using
- the visible portions of any associated sequence alignments. A
- message in the structure viewer's status bar will be shown if not
- enough aligned columns were available to perform a superposition.
- </p>
- <p>
- See the <a href="jmol.html">Jmol
- </a> and <a href="chimera.html">Chimera</a> help pages for
- more information about their capabilities.</p>
-
-
- <p>
- <strong>Retrieving sequences from the PDB</strong><br>You can
- retrieve sequences from the PDB using the <a
- href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
- retrieved with this service are derived directly from the PDB 3D
- structure data, which can be viewed in the same way above. Secondary
- structure and temperature factor annotation can also be added. <br />
-
- <br>Jalview will also read PDB files directly - either in PDB
- format, or <a href="mmcif.html">mmCIF</a>. Simply load in the file
- as you would an alignment file. The sequences of any protein or
- nucleotide chains will be extracted from the file and viewed in the
- alignment window.
- </p>
-
- <p>
- <strong>Associating a large number of PDB files to
- sequences in an alignment</strong><br /> It is often the case when working
- with structure alignments that you will have a directory of PDB
- files, and an alignment involving one or more of the structures. If
- you drag a number of PDB files onto an alignment in the Jalview
- desktop, Jalview will give you the option of associating PDB files
- with sequences that have the same filename. This means, for example,
- you can automatically associate PDB files with names like '1gaq.pdb'
- with sequences that have an ID like '1gaq'. <br /> <em>Note:
- This feature was added in Jalview 2.7</em>
- </p>
- <p>
- <em>Note for Jalview applet users:<br> Due to the applet
- security constraints, PDB Files can currently only be imported by
- cut and paste of the PDB file text into the text box opened by the
- 'From File' entry of the structure menu.
- </em>
- </p>
-
- <p>
- <strong>Viewing the PDB Residue Numbering</strong><br>
- Sequences which have PDB entry or PDB file associations are
- annotated with sequence features from a group named with the
- associated PDB accession number or file name. Each feature gives the
- corresponding PDB Residue Number for each mapped residue in the
- sequence. The display of these features is controlled through the <strong>"View→Sequence
- Features"</strong> menu item and the <a href="featuresettings.html">Feature
- Settings dialog box</a>.
- </p>
- <br />
- <hr>
- <p>
- <strong>Switching between mmCIF and PDB format for
- downloading files from the PDB</strong><br /> Jalview now employs the <a
- href="mmcif.html">mmCIF format</a> for importing 3D structure data
- from flat file and EMBL-PDBe web-service, as recommended by the
- wwwPDB. If you prefer (for any reason) to download data as PDB files
- instead, then first close Jalview, and add the following line to
- your .jalview_properties file:<br />
- <code> PDB_DOWNLOAD_FORMAT=PDB </code>
- <br /> When this setting is configured, Jalview will only request
- PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
- file support was added in Jalview 2.10.</em>
- </p>
-
- <p>
- <em><strong>Outstanding problem with cut'n'pasted
- files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
- via the cut'n'paste dialog box will not be correctly highlighted
- or coloured when they are displayed in structure views, especially
- if they contain more than one PDB structure. See the bug report at
- http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>
- </p>
-
-</body>
-</html>
-
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