Annotated residue selections
[Menu-bar>Tutorials] Residue annotations, allow the assignment of information to specific
amino acids or nucleotides of proteins.
They are special types of residue selections.
A residue annotation has a list of entries each having a name, some
user typed text and a toggle button.
The user can change these entries and add new entries.
The entries can contain several types of information:
- Rendering commands for 3D-viewers,
- LaTeX-code for the PDF-output,
- Hyperlinks, PUBMED-references, database references,
- Notes, for example literature citations, experimental conditions.
A ResidueAnnotation can be created in different ways:
- A residue selection can be created by dragging the mouse over the sequence. Right-click opens the context menu of the residue
selection. With the menu item
[Residue-selection-contextmenu] a
residue annotation can be created that has the same amino acid
positions.
- The alignment cursor is positioned on a residue selection. The
tool-button
is used to
create a residue annotations.
- The cursor is placed on the residue under consideration and the tool-button is pressed.
Residue annotations which are highlighted in the alignment can be selected in two different ways: By CTRL left-click or by dragging a rectangular box.
Selected residue annotations have .
Sequence Features:
Features like phosporylation sites and active sites are special
annotations which are retrieved from a computational service and are
therefore not saved to hard disk. Their color cannot be changed.
Background Images
Image icons are a visual aid to recognize proteins and residue
annotations. They are associated to proteins or annotations by
(See http://www.bioinformatics.org/strap/dragProteinLink.html).
Supported formats are gif, png, bmp and jpg.
Images in Web pages within the Web browser can only be dragged if they
do not serve as a hyper-link.
Obtaining icons:
Species Icons:
Some protein files have a record of the species name.
These species names can be used to set a suitable icon for the selected proteins:
.
Structure Icons:
To download the 3d-structure thumb-nails from the PDB and use them as icons for the selected proteins,
press this button:
.
To delete the icons of all selected proteins press this button:
.
Mapping of species and icons: A customizable table that maps species to images can be inspected:
To deactivate an icon type, associated "NONE".
To see a list of currently loaded images press
.