PyMOL's settings infrastructure is about halfway through a major overhaul. Previously, there was only one settings database for the entire program and all settings were floating point numbers. Now settings can be of several different types, and every state and every object can have an optional set of distinct settings. However, much of the internal code has yet to be modified to take advantage of these new features, so many object and state specific settings won't yet have the desired effect. This work should be completed by version 0.60 at the latest.
In addition, there are some settings names which should be revised because they are misleading or confusing. Therefore, expect some setting names and functions to change up through release 0.70.
The "set" command is used to change settings. See "help set" or the reference section for more information.
set stick_radius,0.1 # global set stick_radius,0.2,prot # object specific set stick_radius,0.3,prot,3 # object and state specific
Because the names and functions of settings are still somewhat in flux, they are simply listed here without description. Your best bet is to avoid relying on these until we approach the 1.0 release. However, an attempt will be made to support old settings names in the new releases.
You can always view the current settings database using the "Edit All..." option of the "Settings" menu
all_states ambient ambient_scale antialias auto_zoom autohide_selections autoshow_lines autoshow_nonbonded autoshow_selections backface_cull bg_rgb bonding_vdw_cutoff button_mode cache_display cache_frames cartoon_debug cartoon_dumbbell_length cartoon_dumbbell_radius cartoon_dumbbell_width cartoon_fancy_helices cartoon_fancy_sheets cartoon_flat_sheets cartoon_loop_quality cartoon_loop_radius cartoon_oval_length cartoon_oval_quality cartoon_oval_width cartoon_power cartoon_power_b cartoon_rect_length cartoon_rect_width cartoon_refine_normals cartoon_round_helices cartoon_sampling cartoon_smooth_loops cartoon_tube_quality cartoon_tube_radius cavity_cull cgo_ray_width_scale cull_spheres dash_gap dash_length dash_radius dash_width depth_cue direct dist_counter dot_density dot_hydrogens dot_mode dot_size dot_width fast_idle fog gamma half_bonds hash_max idle_delay internal_gui internal_gui_width isomesh_auto_state label_color light line_radius line_smooth line_width max_triangles mesh_radius mesh_width min_mesh_spacing movie_delay no_idle nonbonded_size normal_workaround orthoscopic overlay pickable power ray_trace_fog ray_trace_fog_start ray_trace_frames reflect ribbon_power ribbon_power_b ribbon_radius ribbon_sampling ribbon_width rock_delay sel_counter selection_overlay selection_width shininess single_image slow_idle solvent_radius spec_power spec_reflect specular sphere_quality spheroid_fill spheroid_scale spheroid_smooth static_singletons stereo_angle stereo_shift stick_nub stick_overlap stick_quality stick_radius surface_best surface_normal surface_proximity surface_quality sweep_angle sweep_speed test1 test2 text trim_dots valence