Working with annotation from 3D structure data

Jalview can process PDB data associated with sequences to display values extracted from the Temperature Factor column for corresponding sites, and secondary structure from DSSP or RNAView (as appropriate).

Extracting data from PDB files
Annotation is created for structure files retrieved directly from the PDB loaded from the file system (via the Structure→Associate Structure...→From file option, or when displayed via the View Structures Menu.
Structure annotation is not automatically added to an alignment, but any available structure annotation rows for the current selection or a particular sequence can be added via the Add Reference Annotation in the Selection and Sequence ID sub-menus of the Sequence ID Panel's popup menu.
Please note:Protein structures are analysed in situ, but Jalview employs a web service to process RNA structures which can cause long delays if your internet connection is slow.

The Annotations alignment menu provides settings useful for controlling the display of secondary structure annotation.

Shading sequences by associated structure annotation
The annotation colouring dialog (opened by the Colour→By Annotation option) allows sequences with associated secondary structure data to be shaded according to secondary structure type. Once the dialog is opened, select the Per Sequence option and then choose Secondary structure from the dropdown menu.
When colouring alignments by secondary structure, two modes can be employed. The default is to shade sequences with the same colour as the secondary structure glyph. If, however, original colours is selected and another colourscheme has already been applied, then only portions of the sequence with defined secondary structure will be shaded with the previously applied scheme.

Configuration options for processing PDB files
Occasionally, you may wish to disable secondary structure processing. Configuration options in the Structure tab in the Tools→Preferences dialog allow the processing of structure data to be disabled, or selectively enabled. For more information, take a look at the documentation for the structure panel.

The display of secondary structure data was introduced in Jalview 2.8.2, and is made possible by Jalview's use of Jmol's DSSP implementation, based on the original Kabsch and Sander algorithm ported by Robbie P. Joosten and colleagues, and a client for Fabrice Jossinet's pyRNA services that was developed by Anne Menard, Jim Procter and Yann Ponty as part of the Jalview Summer of Code 2012.