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<head>
<title>PDB Viewing</title>
</head>
<body>
-<p><strong>Viewing PDB Structures</strong></p>
-
-<p>Jalview can view protein structures associated with a sequence
-via the <strong>"Structure→"</strong> submenu from a
-sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.</p>
-<p>The following menu entries are provided for viewing structure data<br>
- <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.
- </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>
+ <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><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>
- <br>
-</p>
+ </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>If a single pdb
+<p>If a <strong>single</strong> PDB
structure is selected, one of the following will happen:</p>
<ul>
<li>If no structures are open, then an interactive display of the
- structure will be opened in a new window</li>
+ structure will be opened in a new window.</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>
+ 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
- PDB viewer</a> help page for more information about the display.</li>
+ </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
</ul>
- <p><strong>Associating PDB files with Sequences</strong></p>
- <p>To associate PDB files with a sequence, right click on a sequence
-ID and select "Structure<strong>→</strong> Associate Structure with
-Sequence", and one of the submenus:</p>
-<ul>
- <li>From File - You can 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>Enter PDB Id - Jalview will use WSDBFetch, provided by the
- EBI, to fetch the PDB file with the entered Id.<br>
- </li>
-
- <li>Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the
- EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.</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="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
+ 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
+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>
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>
+<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>
git://source.jalview.org / jalview.git / blobdiff