Atom selection

7.1 Atom selection

You can hide and/or show atoms using the menu items in View Select 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, by proximity and slice. This dialog box can be opened selecting the View Select Custom item in the main menu.
All four operating modes share some input fields. You can create a totally new selection or you can update a pre-existing selection, clicking the Normal or Additive item in the Selection box. The box placed at right window corner 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 one selects all hydrogens, the second one selects the backbone atoms and the third one selects the water molecules. Checking Invert, the meaning of the above buttons is inverted (e.g. clicking Hydrogens, all hydrogen atoms are unselected). The Display box contains controls useful to change the visualization in selective way: you can change the visualization mode (Don't change, Wireframe, CPK dotted, CPK wireframe, CPK solid, Ball & stick wireframe, Ball & stick solid, Stick wireframe, Stick solid, Tube and Trace) and the color of groups of atoms. This last option is enabled only if Change color is checked. For more information, see the Display modes section.

7.1.1 Selection by atom(s)

Select by atom name When the Atoms tab is selected, it's possible show ( button) or hide ( button) one or more atoms, using the Selection field in which the selection must be in the following 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-fields are 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, you can pick it clicking the structure in the main window or selecting Atom Select / Hide in the context menu or 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

The Reset button cleans the Selection field.

7.1.2 Selection by range

Select by range This operating mode is useful to select more than one atom in sequence. You can specify the starting and the ending atom/residue number, completing the Range fields or clicking the structure in the main window. The and buttons have the same function explained above.

7.1.3 Using the proximity tool

Proximity tool This selection mode is useful to un/select the atoms or residues (see What box) around an atom, residue, chain and molecule (see Around box). You must specify the radius (see Radius field) of the sphere/spheroid and its object center in the Selection field. Using the and buttons, you can select or unselect the atoms or the residues contained in the spheroid.

7.1.4 Slice selection

Slice selection With the Slice tab, you can un/select atoms, residues, chains and molecules inside a user-defined slice: you can specify the selection Mode (Atom, Residue, Chain and Molecule), the cut Plane (XY, YZ, ZX), the slice Thickness in Å and the slice Position. The and buttons have the same function as in the other selection modes.