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).
-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.
++ Viewing PDB Structures +
+ Jalview can be used to view protein structures by following the steps + below: ++ 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. +
+ ++ If a single PDB structure is selected, one of the + following will happen: +
+ +
+ 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 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.
+
+ 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.
+