</head>
<body>
<p>
- <strong>Discovering and Viewing PDB Structures</strong>
+ <strong>Discovering and Viewing PDB and 3D-Beacons structures</strong>
</p>
Jalview can be used to explore the 3D structures of sequences in an
alignment by following the steps below:
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
+ <li>If one or more structures exist in the PDB for the given
sequence, the <a href="structurechooser.html">Structure
Chooser</a> dialog will open with them listed in the results
pane.
href="structurechooser.html">Structure Chooser</a> interface
will present options for manual association of PDB structures.
</li>
+ <li>
+ Since Jalview 2.11.2 you can also search the 3D-Beacons Network
+ for structures. The 3D-Beacons Network acts as a one-stop shop for protein
+ structures by combining and standardising data from several providers.
+ See <a href="structurechooser.html#3dbeaconssearch">3D-Beacons Search</a> for
+ instructions.
+ </li>
</ul>
</li>
- <li><strong>Selecting Structures</strong><br />You can select
+ <li><strong>Selecting PDB Structures</strong><br />
+ If one or more structures have been found from the PDB, you can select
the structures that you want to open and view by selecting them
with the mouse and keyboard.<br />By default, if structures were
discovered, then some will already be selected according to the
<strong>Structure Viewers in the Jalview Desktop</strong><br /> 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
+ provided it is installed and can be launched by Jalview. ChimeraX and PyMOL
+ support is included from Jalview 2.11.2. The default
viewer can be configured in the <a href="preferences.html#structure">Structure
tab</a> in the <strong>Tools→Preferences</strong> dialog box.
for more information.
</p>
<p>
- <img src="schooser_viewbutton.png"
- style="width: 465px; height: 81px" /><br/> <strong><a
+ <strong><a
name="afterviewbutton">Controlling where the new structures
will be shown</a></strong>
+ <br/>
+ <img src="schooser_viewbutton.png" />
<br />The Structure Chooser offers several options
- for viewing a structure. <br/><strong>New View</strong> will open a new
+ for viewing a structure. <br/>
+ The <strong>Open new structure view</strong> button will open a new
structure viewer for the selected structures, but if there are views
already open, you can select which one to use, and press the <strong>Add</strong>
button. Jalview can automatically superimpose new structures based
git://source.jalview.org / jalview.git / blobdiff