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<head>
<title>PDB Viewing</title>
</head>
<body>
-<p><strong>Viewing PDB Structures</strong></p>
+ <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>
-<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>
+ </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
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>
- <li><a name="viewreps"/>The <strong>"Structure→View all <em>N</em>
+ <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>
+</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
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