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:
++ Jalview can view protein structures associated with a sequence via the + "Structure→" submenu from a sequence's pop-up menu. +
+ 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. +
+The following menu entries are provided for viewing structure data
+
If a single pdb +structure is selected, one of the following will happen:
+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).
-Sequences which have PDB File associations are annotated with sequence features - from the group 'PDBFile' giving the corresponding PDB Residue Number for each - mapped residue in the seuqence. The display of these features is controlled through - the "View→Sequence Features" menu item and the - Feature Settings dialog box.
-See the PDB Viewer help page for more information.
+Associating PDB files with Sequences
+To associate PDB files with a sequence, right click on a sequence +ID and select "Structure→ Associate Structure with +Sequence", and one of the submenus:
+ +Importing PDB Entries or files in PDB format
+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).
+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
+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.
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.