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.