Viewing PDB Structures
-Jalview can view protein structures associated with a sequence via the "Structure→View - PDB entry:" entries from a sequence's pop-up menu. This will open an - interactive display of the structure in a new window, or prompt you - to associate the sequence with an existing view of the selected - structure. See the Jmol PDB viewer help page - for more information about the display. -
-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.
-
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 seuqence. The
-display of these features is controlled through the
-"View→Sequence Features" menu item
-and the Feature Settings dialog
-box.
+ 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.
+
+ Importing PDB Entries or files in mmCIF format
+ mmCIF file format provides an alternative means for
+ importing 3D structure data from flat file and EMBL-PDBe
+ web-service. To enable mmCIF as the default format for
+ importing PBD sequences from the PDB sequence fetcher, add or modify the
+ property
+ DEFAULT_STRUCTURE_FORMAT=mmCIF in Jalview properties file.
+ Once this is done, the steps followed in retrieving PDB format files above can
+ be followed to obtain the same data with mmCIF. mmCIF format file support was added in Jalview 2.9.1.
+ 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.
+