Viewing PDB Structures
-Jalview has a simple 3D structure viewer which can visualize polypeptide backbone - structures associated with a sequence in a particular alignment view. It is - accessed via the "Sequence→View PDB - entry:" entry from the sequence's pop-up menu.
-To associate PDB files with a sequence, right click on a sequence ID and select - "Associate Structure with Sequence", and one of the submenus:
-Note: You can retrieve sequences from the PDB using the Sequence Fetcher. 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).
-See the PDB Viewer help page for more information.
++ Discovering and Viewing PDB Structures +
+ Jalview can be used to explore the 3D structures of sequences in an + alignment by following the steps below: +
+ 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. 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. +
+
+ After pressing the
+ 'View' button in the Structure Chooser
The behaviour of
+ the 'View' button depends on the number of structures selected, and
+ whether structure views already exist for the selected structures or
+ aligned sequences.
+
If multiple structures are selected, then Jalview will always + create a new structure view. The selected structures will be + imported into this view, and superposed with the matched positions + from the aligned sequences. A message in the structure viewer's + status bar will be shown if not enough aligned columns were + available to perform a superposition.
++ If a single PDB structure is selected, one of the + following will happen: +
+ +
+ 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.
+