</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.
+ <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>
- 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>
+ 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>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>
+ <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>
+ </ol>
The
<a href="jmol.html">Jmol viewer</a> has been included since Jalview
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.
- </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>
- <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> -->
-<p>If a <strong>single</strong> pdb
+<p>If a <strong>single</strong> PDB
structure is selected, one of the following will happen:</p>
<ul>
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>
git://source.jalview.org / jalview.git / blobdiff