- 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. - -
++ 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. + +