Different methods of selecting atoms can be found on the Select panel.

Select Panel

Basic Group

Basic Group


Shortcut: Ctrl-A

Selects all atoms in the current model.


Deselects all atoms in the current model.


Shortcut: Ctrl-I

Inverts the current atom selection, deselecting selected atoms, and selecting deselected ones.


Shortcut:: Ctrl-E

Expands the current atom selection, adding every atom bound to a currently-selected atom.

Intelligent Select Group

Intelligent Select Group

The intelligent select allows ranges or subsets of atoms to be (de)selected by one of several different criteria. The desired atom set should be typed into the Target box, and then those matching atoms Added or Removed from the current selection. Aten attempts to auto-detect the exact type of set/range that is being typed, but this may be overriden using the Type selector.

The specified atom Target may be one of the following:

  • A NETA description of an atom (in which case the element should be specified using the element selection button)
  • An atom index or element, or a range thereof
  • A code snippet
  • Atom type name, optionally containing wildcards (note that this mode cannot be automatically determined, and must be chosen explicitly)

These are explained in more detail below.

NETA Description

A valid NETA description of an atom, excluding its character element which should be specified using the element selection button to the right of the Type selector.



...would target all atoms of the character element specified that are singly-bound to an oxygen atom with one hydrogen.


...would target all atoms of the character element specified that share a double-bond with a carbon atom that is not in a ring.


...would target all atoms of the character element specified that have three methyl groups attached.

Range Selection

A range of atom indices or elements, or an individual atom index or element. A single atom index or element symbol may be prepended or appended with a '+' symbol to denote 'up to' and 'onwards' respectively.



...would target atom indices 1 through 6 inclusive.


...would target all atom indices from 6 and up.


...would target all atom indices up to and including 6.


...would target all atoms that are carbon, nitrogen, oxygen, fluorine, or neon.

Code Select

Executes the supplied snippet of code for each atom - if the result of the code snippet evaluates to true then the atom is targeted. A declaration Atom i; is prepended to the snippet, meaning that atom information can be probed through the variable i.


i.rx > 0.0;

...targets all atoms whose x coordinate is greated than zero.

(i.rz < 4.0 && i.element > C);

...targets all atoms whose z coordinate is lesss than 4.0 Angstroms and that are nitrogens or heavier.

Type Name Selection

Selects atoms based on their assigned type name (not their equivalent name). Wildcards ('*') may be used in the name matching.