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Selections
Selecting Controls
You can select a structure by clicking on any atom of the structure.
First, you should choose the type of selection by using Selecting Controls
(See Figure 8) (c), which is set at none by default. It contains the following options:
1) none, 2) Atoms, 3) Residues, 4) Chains, 5) Segments, and 6) Molecules. In
this case, choose the Residues option. After clicking on an atom of the
molecules 1aaq_red, the residue, which contains this atom, is selected (a).
This selection appears in the Names Panel (b). The default name is (sel01).
It can be processed as any molecule by using the Viewer Menu. In
particular, the selection is shown in sticks.
If you click on another atom, a new residue will be selected and added
to the previous selection. To open a new selection you should disable the last
selection by clicking on its name and start selecting new atoms; a new
selection with the name (sel02) will appear.
Figure 8 - Selecting a
Residue
The Show, Hide, Labels and Color... items in the
Viewer Menu for a selection are the same as for a molecule. The Actions...
item is a bit different and contains additional options. For instance,
you can select atoms around the current selection within some radius. To do
this, select Actions->Around->Atoms within 4A.
Sequence Viewer Button
When dealing with a protein-ligand complex for the first time, it is
very useful to quickly find and display different amino acids and ligands. The
sequence viewer extension allows you to easily choose and display one or more
residues.
Choose the Sequence Viewer Button (See Figure 9) (e). A sequence
of the amino acids (a) will appear on your screen. Selecting Controls will be
changed on the residue item (d).
Use the mouse to click over different residues in the sequence and see
how they are highlighted (a). In addition, the highlighted residue will appear
in your Viewer so that you can visualize it easily. The name of the selections
will appear in the Names Panel (c) Click on a residue to unselect it. Use the Scroll
button (b) to display the entire sequence of residues.
Figure9 - Sequence Viewer
Note: In order to use the sequence for
selecting residues, the Selecting Controls must be set as Residues (d).
Selecting using
the Main Menu
You can select hetatoms, hydrogens, waters and all molecules by choosing
the Edit-> Select... item in the Main Menu.