Select some residues with the mouse

Load the BUTTON:Tutorials#bExampleFiles("INTRO")!. When the mouse is dragged in one row of the alignment panel a residue selection is generated. The selected sequence is copied to the clipboard and can be pasted in Web forms or text programs. It is also passed into all 3D-views like Astex or Pymol. If you move slowly over selected residues in the alignment pane a WIKI:Balloon_help appears. You can open a WIKI:Context_menu by right-clicking the highlighted residues.
Exercise:
  1. Change the color of the mouse selection.
  2. Copy a sequence of amino acids from the alignment into a text program.
  3. Remove the mouse selection.

Annotated residue selection

But this simple selection has two main limitations: The selection cannot store annotations and it is lost after the end of the Strap session. In contrast annotated selections are distinguished by a name and are permanently stored when the alignment is saved.

The mouse selection, can easily be converted into a named selection. Try this by using the context menu item over the mouse selection BUTTON:ResidueSelectionPopup#ACTION_convertToResidueAnnotation in the WIKI:Context_menu.

Residue selection. for the protein under the mouse pointer can also be created using the context menu of the alignment panel. It is presented as a table (see figure).
Figure: Annotated selection of amino acids is shown as a table.
JCOMPONENT:ResidueAnnotationView#docuView()


Exercise:
  1. Mark the active site residue Ser129 in the protein hs_.... and create an annotated residue selection. Change the name of the annotation to "Ser129"
  2. Proceed the same with Ser129 in the protein b1_... .
  3. Add Lys33 by adding "33:" to the row LABEL:ResidueAnnotationView#POS_AA. The colon after the 33 indicates that the number 33 refers to the PDB residue number and not to the the residue index according to the Rasmol/Jmol notation. Add the correct chain identifier directly after the colon.
  4. Use BUTTON:"Add entry" to add more information like notes, remarks and hyper-links to the table.
  5. Create a table row for "3D_view". Subsequently press the "3D_view"-button in the first column of the table.

Selecting residue selections

Single residue selections can be selected and unselected by CTRL+left-Click. They will be indicated by WIKI:Marching_ants. Many residue selections can be selected with SHIFT-left-Click.

Alternatively, residue selections can be selected by opening a box with the mouse. All residue selections within the box are selected. According to the Graphic program Gimp, residue selections can be added and removed with SHIFT (union set) and CTRL (cut-set).

Background Images

Image icons can be dragged from the desktop the file browser, and from Web-pages. Check out