auto_color (boolean, default: on) controls whether or not new objects are given a different color for their carbon atoms.

auto_copy_images (boolean, default: on) controls whether or not PyMOL automatically copies images from the OpenGL viewport into the system's clipboard.

auto_defer_builds (integer, default: 500) Multistate models with fewer than auto_defer_builds number of states will automatically be preprocessed for geometry and rendering. Set to -1 to process all states regardless of count.

auto_dss (boolean, default: on) controls whether or not secondary structure is automatically computed for structure which lack such definitions.

auto_overlay (boolean, default: off) controls whether or not overlay text is automatically shown/hidden in response to user actions.

auto_rename_duplicate_objects (boolean, default: off) if on, PyMOL will rename new objects that have the same name as an existing object; if off, PyMOL will overwrite the existing object.

auto_show_lines (boolean, default: on) controls whether or not the lines representation is automatically shown for new objects.

auto_show_nonbonded (boolean, default: on) control whether or not the nonbonded representation is automatically shown for new objects.

auto_show_selections – see selections

auto_show_spheres (boolean, default: off) controls whether or not the sphere representation is automatically shown for new objects.

autoclose_dialogs (boolean, default: on) Unused setting.

legacy_vdw_radii (boolean, default: off) controls whether or not old VDW radii are used.

multiplex (integer, default: -1) controls whether or not multi-state objects are loaded into one object or multiple objects.

preserve_chempy_ids (boolean, default: off) controls whether or not Chemical Python objects are loaded with their identifiers preserved.

rank_assisted_sorts (boolean, default: on) controls whether or not the position of an atom in the input file is using in the sorting algorithm.

retain_order (boolean, default: off) controls whether or not PyMOL sorts atoms internally.

security (integer, default: 1) is an internal setting.