6.1 Atom selection | ![]() |
The user can hide and/or show the atoms using the
menu items in View -> Select (click here
for more information) in order to change the properties of the visible atoms
only (e.g. color,
measure, etc). If the predefined selections are insufficient, it's possible to create a
custom selection, that can be made by atom specification, by range and by
proximity. This dialog box can be opened selecting the View ->
Select -> Custom item from the main menu.
Some functions are common to all three operating modes. The user can make a new
selection from the beginning or he can update an old selection clicking the Normal
or Additive item of the Selection box. The box placed at the right
window side contains the control buttons: All selects all atoms, None
deselects all atoms, Invert inverts the selection,
and
adds/removes the atoms using the selected criteria. The Hydrognens, Backbone
and Water buttons are for fast selections: the first selects all
hydrogens, the second select the backbone atoms and the third select the water
molecules. Checking Invert, the meaning of the above buttons is inverted
(e.g. clicking Hydrogens, all hydrogen atoms are unselected). The
button closes the dialog box.
6.1.1 Selection by atom(s)
When the Atoms sheet is selected, it's possible show ( button) or hide (
button) the atom(s) specified in the Selection field with the
format:
AtomName : ResidueName : ResidueNumber : Chain : MoleculeNumber
The maximum length of each sub-field is four characters, but the Chain
sub-field requires only one. The selection can contain wildcards (* and ?) and all
sub-fields are optional from left to right. The omitted sub-field is equivalent to *.
Clicking the items in Atom, Residue, Number, Chain
and Mol. columns, the Selection field is automatically completed.
To un/select a single atom, the user can pick it clicking the structure in the main
window. Another way to made the same operation, is typing the atom number in the Selection
field.
Examples:
12 | un/select the the atom # 12 | |
C* | un/select all carbons | |
*:ARG | un/select all arginines | |
H*:TYR | un/select the hydrogens of all tyrosines | |
*:*:146 | un/select the residue 146 (in all molecules) | |
*:*:2? | un/select the residue range from 20 to 29. | |
*:A*:*:B | un/select all residues beginning with "A" as name present in the B chain | |
*:*:*:*:1 | un/select all atoms of the first molecule | |
*:*:*:C:2 | un/select the C chain of the second molecule |
Clicking the Reset button, the Selection field is cleared.
6.1.2 Selection by range
This operating mode is useful to select more than one atom in
sequence. The user can specify the starting and the ending atom/residue number, typing in Range
fields or clicking the structure in the main window. The and
buttons have the same function
explained in the previous section.
When the un/selection is done, press button to close the dialog
box.
6.1.3 Using the proximity tool
This selection mode is useful to un/select the atoms or residues (see What box) around an atom, a residue, a chain and a molecule (see Around box).
The user must
specify the radius (see Radius field) of the sphere/spheroid and its
object center in the Selection field. Using the and
buttons,
the user can select or unselect the atoms or the residues contained in the
spheroid.