6.1 Atom selection OpenGL

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 Close button closes the dialog box.

 

6.1.1 Selection by atom(s)

Select by atom name

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.

Select by range

When the un/selection is done, press Close 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).

Proximity tool

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.