- 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:
+ 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. +
-+ If a single PDB structure is selected, one of the + following will happen: +
-Associating PDB files with Sequences
-Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the "View Structure" option is selected - from a sequence's pop-up menu. Jalview uses the sequence's ID to query the PDB Rest API, provided by the - EBI to discover PDB ids associated with the sequence.
- -Manual association of PDB files with Sequences
-To manually associate PDB files with a sequence, right click on a sequence -ID and select the "View Structure" option, this opens the 'Structure Chooser' dialogue. Then pick any of the follwing options listed below from the drop-down menu in the 'Structure Chooser' panel to proceed with manual association: +
+ 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 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.
+ 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.
+ 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.
+ 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.
+ 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.
+