active_selections (boolean, default: on) controls whether or not PyMOL relies upon the concept of an active selection.

atom_name_wildcard (string, default: '') controls the wildcard character used when matching atom names. If this string is empty, then the normal wildcard setting will be used. The practical purpose of this setting is to disable use of asterisks as an atom name wildcard when PDB structures are loaded with asterisks in atom names.

auto_classify_atoms (boolean, default: on) controls whether or not PyMOL spends extra CPU cycles classifying atoms as polymer, organic, solvent, or inorganic as well as locating per-residue guide atoms.

auto_hide_selections (boolean, default: on) controls whether or not PyMOL automatically disables selections when new objects or selections are created.

auto_indicate_flags (boolean, default: on) controls whether or not PyMOL automatically indicates flagged atoms when the “flag” command is issue.

auto_number_selections (boolean, default: off) controls whether PyMOL gives each new unnamed selection a unique name or whether it simply uses “sele”.

auto_show_selections (boolean, default: on) controls whether or not PyMOL automatically enables each new selection.

ignore_case (boolean, default: on) controls whether or not PyMOL ignores the case of symbols, commands, and operators – note that it is not entirely effective at present.

sel_counter (integer, default: 0) when auto_number_selections is on, this setting tracks the number of the last selection created.

selection_overlay (integer, default: on) controls whether the visual selection indicators are overlayed on top of the 3D geometry or drawn together with them, in which case they may be hidden by the atom representation.

selection_round_points (boolean, default: on) controls whether the selection indicators are drawn as square or round points.

selection_visible_only (boolean, default: off) controls whether all selected atoms are indicated or only those with at least one visible representation.

selection_width (float, default: 3.0) controls the minimum width of selection indicators in pixels.

selection_width_max (float, default: 10.0) controls the maximum width of selection indicators in pixels.

selection_width_scale (float, default: 2.0) controls the rate at which selection indicators are scaled.

wildcard (string, default: *) controls the wildcard character used in matching selections.