Discovering and Viewing PDB and 3D-Beacons structures

1. Select the "3D Structure Data..." option from a sequence's pop-up menu to open the Structure Chooser dialog box.
   • If one or more structures exist in the PDB for the given sequence, the Structure Chooser dialog will open with them listed in the results pane.
   • However, if no structure was found, the Structure Chooser interface will present options for manual association of PDB structures.
   • 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 3D-Beacons Search for instructions.
2. Selecting PDB Structures
   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.
   By default, if structures were discovered, then some will already be selected according to the criteria shown in the drop-down menu. The default criteria is 'highest resolution', simply choose another to pick structures in a different way.
   
   • Viewing Cached Structures
     If previously downloaded structures are available for your sequences, the structure chooser will automatically offer them via the Cached Structures view. If you wish to download new structures, select one of the PDBe selection criteria from the drop-down menu.
3. To view selected structures, click the "View" button.
   
   • Additional structure data will be downloaded with the EMBL-EBI's dbfetch service
   • SIFTS records will also be downloaded for mapping UniProt protein sequence data to PDB coordinates.
   • A new structure viewer will open, or you will be prompted to add structures to existing viewers (see below for details).

Structure Viewers in the Jalview Desktop
The Jmol viewer has been included since Jalview 2.3. Jalview 2.8.2 included support for Chimera, 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 Structure tab in the Tools→Preferences dialog box.

Structure data imported into Jalview can also be processed to display secondary structure and temperature factor annotation. See the Annotation from Structure page for more information.

Controlling where the new structures will be shown

The Structure Chooser offers several options for viewing a structure.
The Open new structure view 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 Add button. Jalview can automatically superimpose new structures based on the linked alignments - but if this is not desirable, simple un-tick the Superpose Structures checkbox.

Superposing structures
Jalview superposes structures using the currently selected columns (if more than 3 columns are selected), or the visible portions of any associated sequence alignments. Depending on the viewer, Root Mean Squared Deviation (RMS or RMSD) for each pair of superpositions may be output in the structure viewer's console.

A message in the structure viewer's status bar will be shown if not enough aligned columns were available to perform a superposition.

See the Jmol, Chimera/X and Pymol help pages for more information about their individual capabilities.

Retrieving sequences from the PDB
You can retrieve sequences from the PDB using the Sequence Fetcher. The sequences retrieved with this service are derived directly from the PDB 3D structure data, which can be viewed in the same way above. Secondary structure and temperature factor annotation can also be added.

Jalview will also read PDB files directly - either in PDB format, or mmCIF. Simply load in the file as 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.

Associating a large number of PDB files to sequences in an alignment
It is often the case when working with structure alignments that you will have a directory of PDB files, and an alignment involving one or more of the structures. If you drag a number of PDB files onto an alignment in the Jalview desktop, Jalview will give you the option of associating PDB files with sequences that have the same filename. This means, for example, you can automatically associate PDB files with names like '1gaq.pdb' with sequences that have an ID like '1gaq'.
Note: This feature was added in Jalview 2.7

Note for Jalview applet users:
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.

Viewing the PDB Residue Numbering
Sequences which have PDB entry or PDB file associations are annotated with sequence features from a group named with the associated PDB accession number or file name. Each feature gives the corresponding PDB Residue Number for each mapped residue in the sequence. The display of these features is controlled through the "View→Sequence Features" menu item and the Feature Settings dialog box.

Switching between mmCIF and PDB format for downloading files from the PDB
Jalview now employs the mmCIF format for importing 3D structure data from flat file and EMBL-PDBe web-service, as recommended by the wwwPDB. If you prefer (for any reason) to download data as PDB files instead, then first close Jalview, and add the following line to your .jalview_properties file:
PDB_DOWNLOAD_FORMAT=PDB
When this setting is configured, Jalview will only request PDB format files from EMBL-EBI's PDBe.
mmCIF format file support was added in Jalview 2.10.

Outstanding problem with cut'n'pasted files in Jalview 2.6 and Jalview 2.7
Structures imported via the cut'n'paste dialog box will not be correctly highlighted or coloured when they are displayed in structure views, especially if they contain more than one PDB structure. See the bug report at http://issues.jalview.org/browse/JAL-623 for news on this problem.