</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>.
+ <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 <strong>'Structure Chooser'</strong>
- dialogue is opened with a list of the found structures meta-data.</li>
- <li>However, if no structure was found, the <strong>'Structure Chooser'</strong> dialogue is opened with options for manual association of PDB structures.</li>
+ <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>Choose the structure to view from the presented structures
- summary list. This can be done either manually by clicking directly
- on the desired structure from the list, or automatically by
- using the filter combo-box which enables filtering on certain
- criteria like quality, resolution, etc. The best structure for the chosen criteria is automatically selected by the filtration process. </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>
<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>Associating PDB files with Sequences</strong></p>
- <p>Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the <strong>"View Structure"</strong> option is selected
- from a sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Jalview uses the sequence's ID to query the PDB Rest API, provided by the
- EBI to discover PDB ids associated with the sequence. </p>
-
- <p><strong>Manual association of PDB files with Sequences</strong> </p>
- <p>To manually associate PDB files with a sequence, right click on a sequence
-ID and select the <strong>"View Structure"</strong> option, this opens the <strong>'Structure Chooser'</strong> dialogue. Then pick any of the follwing options listed below from the drop-down menu in the <strong>'Structure Chooser'</strong> panel to proceed with manual association:
-
-<ul>
- <li><strong>From File</strong> - 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><strong>Enter PDB Id</strong> - Jalview will use the PDB Rest API, provided by the
- EBI, to fetch the PDB file with the entered Id.<br>
- </li>
-</ul>
-<strong>Note:</strong> The drop-down menu in the 'Structure Chooser' panel may contain other options employed for filtering structures when one or more structures are auto-discovered.
<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