<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>PDB Viewing</title>
</head>
<body>
- <p>
- <strong>Viewing PDB Structures</strong>
- </p>
- Jalview can be used to view protein structures by following the steps below:
- <ol>
- <li>Select the <strong>"View Structure"</strong> option from a
- sequence's <a href="../menus/popupMenu.html">pop-up menu</a> to invoke the <a href="structurechooser.html">Structure Chooser</a> interface.
- <ul>
- <li>If one or more structures exists for the given sequence, the <a href="structurechooser.html">Structure Chooser</a>
- dialogue is opened with a list of the found structures meta-data.</li>
- <li>However, if no structure was found, the <a href="structurechooser.html">Structure Chooser</a> interface is opened with options for manual association of PDB structures.</li>
- </ul>
- </li>
- <li>Choose the structure to view from the discovered list. This can be done either manually by clicking directly
- on the desired structure(s) in the list, or automatically by
- using the drop-down menu on the interface to filter and auto-select the best structure based on certain
- criteria like quality, resolution, etc.</li>
- <li>When the desired structure(s) have been selected, they can be
- viewed by clicking the <strong>"View"</strong> button below the summary list.
- </li>
-
- </ol>
-
- 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>The following menu entries are provided for viewing structure data
- <ul>
- <li>The <strong>"Structure→View
- Structure→</strong> submenu allows a single PDB structure to be chosen
- for display from the available structures for a sequence.
+ <p>
+ <strong>Viewing PDB Structures</strong>
+ </p>
+ Jalview can be used to view protein structures 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>The <strong>"Structure→View all <em>N</em>
- structures
- </strong> option will open a new window containing all structures associated
- with the current selection, superposed according to the currently selected region of the alignment.<br/><em>This
- capability was added in Jalview 2.7</em>
+ <li><strong>Selecting Structures</strong><br /> If structures
+ have been discovered, then some will already be selected according
+ to predefined selection criteria, such as structures with the
+ highest resolution. Use the drop down menu to select structures
+ according to different criteria, or, alternatively, choose
+ structures manually by selecting with the keyboard and mouse.
+ <ul>
+ <li><strong>Viewing Cached Structures</strong><br />If you
+ have previously downloaded structures for your sequences, they
+ can be viewed by selecting the <strong>Cached PDB
+ Entries</strong> option from the drop down menu at the top of the
+ dialog box.</li>
+ </ul></li>
+ <li>To view selected structures, click the <strong>"View"</strong>
+ button.
</li>
- <li>The <strong>"Structure→View all <em>N</em>
- representative structures
- </strong> option will open a new window containing exactly one structure per
- currently selected sequence.<br />
- <em>The View representative structures option was introduced in
- Jalview 2.8.1</em></li>
- </ul>
-</p> -->
+ </ol>
-<p>If a <strong>single</strong> pdb
-structure is selected, one of the following will happen:</p>
+ 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>
-<ul>
- <li>If no structures are open, then an interactive display of the
- structure will be opened in a new window.</li>
+ <p>
+ If a <strong>single</strong> PDB structure is selected, one of the
+ following will happen:
+ </p>
- <li>If another structure is already shown for the current
- alignment, then you will be asked if you want to add and <a
- href="jmol.html#align">align this structure</a> to the structure in
- the existing view. (<em>new feature in Jalview 2.6</em>).</li>
+ <ul>
+ <li>If no structures are open, then an interactive display of
+ the structure will be opened in a new window.</li>
- <li>If the structure is already shown, then you will be prompted
- to associate the sequence with an existing view of the selected
- structure. This is useful when working with multi-domain or multi-chain PDB files.</li>
+ <li>If another structure is already shown for the current
+ alignment, then you will be asked if you want to add and <a
+ href="jmol.html#align"
+ >align this structure</a> to the structure in the existing view. (<em>new
+ feature in Jalview 2.6</em>).
+ </li>
+
+ <li>If the structure is already shown, then you will be
+ prompted to associate the sequence with an existing view of the
+ selected structure. This is useful when working with multi-domain
+ or multi-chain PDB files.</li>
- <li style="list-style: none">See the <a href="jmol.html">Jmol
- </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
-</ul>
+ <li style="list-style: none">See the <a href="jmol.html">Jmol
+ </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
+ more information about the display.
+ </li>
+ </ul>
-<p><strong>Importing PDB Entries or files in PDB format</strong><br>
-You can retrieve sequences from the PDB using the <a
- href="pdbsequencefetcher.html">Sequence Fetcher</a>. Any sequences retrieved with
-this service are automatically associated with their source database
-entry. For PDB sequences, simply select PDB as the database and enter
-your known PDB id (appended with ':' and a chain code, if desired).<br>
-Jalview will also read PDB files directly. Simply load in the file as
-you would an alignment file. The sequences of any peptide chains will be
-extracted from the file and viewed in the alignment window.</p>
+ <p>
+ <strong>Importing PDB Entries or files in PDB format</strong><br>
+ You can retrieve sequences from the PDB using the <a
+ href="pdbsequencefetcher.html"
+ >Sequence Fetcher</a>. Any sequences retrieved with this service are
+ automatically associated with their source database entry. For PDB
+ sequences, simply select PDB as the database and enter your known
+ PDB id (appended with ':' and a chain code, if desired).<br>
+ Jalview will also read PDB files directly. 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>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>
+ <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>
-<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>
+ <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>
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