Section 3: Selecting parts of the structure
Geneious provides a convenient way to select parts of the structure. This is useful to allow you to highlight features or regions of the structure. At the bottom of the selection window are two buttons labelled Expand All and Collapse All. Clicking Expand All will expand the selection tree to its maximum allowing you to select individual atoms. Click the Expand All button and scroll down the window. Notice how the tree expands to show the chain, residues and atoms. If you click the Highlight button, any selected region will have a yellow halo. For example, select the first residue (1 LYS) with highlighting selected and you will easily be able to see where this Lysine residue is. Similarly, selecting 5 CB within that residue will highlight just the β-carbon atom.
You can also expand and contract parts of the tree by clicking on the arrow to the left of the element you are looking at. Collapse the whole tree by clicking Collapse All. Now click the arrow next to Chain A and note that it expands out to the next level. You can now easily select individual residues without worrying about the atoms that make them up.
You can also select multiple residues by holding the CTRL key on Windows/Linux or Command key on a Mac. Now if you click several residues, each will be selected and you can keep adding to the selection in this way. You can also select a range by holding down the Shift key. Hold Shift, click 1 LYS and 10 ARG and all residues in between will automatically be selected.
The
Select button is also provided with a range of groups to select such as inverting the current selection. Click it and select Inverse and you should now find that all residues apart from 1 LYS to 10 ARG are selected.
Undoing the damage
By now, you have no doubt made many changes to the orientation, style, colors and so on. To return to the original position you can use the reset options.
- Reset View - return the structure to it's original orientation
- Reset Completely - return view to it's original orientation with default style and color
- Reset to Saved - reload the saved state of the molecule
Section 4: Showing useful information