Settings

PyMOL is incredibly useful because of its flexibility. Almost any setting can be tweaked to give you the ability to make your scenes appear just as you want. Each command usually comes with one or more settings. For example, the ray command comes with 50 settings!

List of settings

Below you will find the list of all known settings (as of this writing). Settings are added all the time, so this list should be updated somehow. Also, see all documented settings.

If you feel like documenting them, and what they do, feel free.

A

active_selections all_states ambient angle_color angle_label_position angle_size animation animation_duration antialias async_builds ati_bugs atom_name_wildcard auto_classify_atoms auto_color auto_copy_images auto_defer_builds auto_dss auto_hide_selections auto_indicate_flags auto_number_selections auto_remove_hydrogens auto_rename_duplicate_objects auto_sculpt auto_show_lines auto_show_nonbonded auto_show_selections auto_show_spheres auto_zoom

B

backface_cull batch_prefix bg_rgb bonding_vdw_cutoff button_mode button_mode_name

C

cache_display cache_frames cache_max cache_memory cache_mode cartoon_color cartoon_cylindrical_helices cartoon_debug cartoon_discrete_colors cartoon_dumbbell_length cartoon_dumbbell_radius cartoon_dumbbell_width cartoon_fancy_helices cartoon_fancy_sheets cartoon_flat_cycles cartoon_flat_sheets cartoon_helix_radius cartoon_highlight_color cartoon_ladder_color cartoon_ladder_mode cartoon_ladder_radius cartoon_loop_cap cartoon_loop_quality cartoon_loop_radius cartoon_nucleic_acid_color cartoon_nucleic_acid_mode cartoon_oval_length cartoon_oval_quality cartoon_oval_width cartoon_power cartoon_power_b cartoon_putty_quality cartoon_putty_radius cartoon_putty_range cartoon_putty_scale_max cartoon_putty_scale_min cartoon_putty_scale_power cartoon_putty_transform cartoon_rect_length cartoon_rect_width cartoon_refine cartoon_refine_normals cartoon_refine_tips cartoon_ring_color cartoon_ring_finder cartoon_ring_mode cartoon_ring_radius cartoon_ring_transparency cartoon_ring_width cartoon_round_helices cartoon_sampling cartoon_side_chain_helper cartoon_smooth_cycles cartoon_smooth_first cartoon_smooth_last cartoon_smooth_loops cartoon_throw cartoon_trace_atoms cartoon_transparency cartoon_tube_cap cartoon_tube_quality cartoon_tube_radius cavity_cull cgo_dot_radius cgo_dot_width cgo_ellipsoid_quality cgo_line_radius cgo_line_width cgo_ray_width_scale cgo_sphere_quality cgo_transparency clamp_colors cone_quality connect_bonded connect_cutoff connect_mode coulomb_cutoff coulomb_dielectric coulomb_units_factor cull_spheres cylinder_shader_ff_workaround

D

dash_color dash_gap dash_length dash_radius dash_round_ends dash_width debug_pick defer_builds_mode defer_updates depth_cue dihedral_color dihedral_label_position dihedral_size direct dist_counter distance_exclusion dot_color dot_density dot_hydrogens dot_lighting dot_mode dot_normals dot_radius dot_solvent dot_width draw_frames

E

editor_auto_dihedral editor_auto_origin editor_label_fragments ellipsoid_color ellipsoid_probability ellipsoid_quality ellipsoid_scale ellipsoid_transparency

F

fast_idle fetch_path field_of_view fit_iterations fit_tolerance float_labels fog fog_start frame full_screen

G

gamma gaussian_b_adjust gaussian_b_floor gaussian_resolution geometry_export_mode gl_ambient gradient_max_length gradient_min_length gradient_min_slope gradient_normal_min_dot gradient_spacing gradient_step_size gradient_symmetry grid_max grid_mode grid_slot group_arrow_prefix group_auto_mode group_full_member_names

H

h_bond_cone h_bond_cutoff_center h_bond_cutoff_edge h_bond_exclusion h_bond_from_proton h_bond_max_angle h_bond_power_a h_bond_power_b half_bonds hash_max hide_long_bonds hide_underscore_names

I

idle_delay ignore_case ignore_pdb_segi image_copy_always image_dots_per_inch internal_feedback internal_gui internal_gui_control_size internal_gui_mode internal_gui_width internal_prompt isomesh_auto_state

L

label_angle_digits label_color label_digits label_dihedral_digits label_distance_digits label_font_id label_outline_color label_position label_shadow_mode label_size legacy_mouse_zoom legacy_vdw_radii light light2 light3 light4 light5 light6 light7 light8 light9 light_count line_color line_radius line_smooth line_stick_helper line_width log_box_selections log_conformations logging

M

map_auto_expand_sym matrix_mode max_threads max_triangles mesh_carve_cutoff mesh_carve_selection mesh_carve_state mesh_clear_cutoff mesh_clear_selection mesh_clear_state mesh_color mesh_cutoff mesh_grid_max mesh_lighting mesh_mode mesh_negative_color mesh_negative_visible mesh_normals mesh_quality mesh_radius mesh_skip mesh_solvent mesh_type mesh_width min_mesh_spacing moe_separate_chains mouse_grid mouse_limit mouse_restart_movie_delay mouse_scale mouse_selection_mode mouse_wheel_scale movie_animate_by_frame movie_delay movie_fps movie_loop movie_rock multiplex

N

no_idle nonbonded_size nonbonded_transparency normal_workaround normalize_ccp4_maps normalize_grd_maps normalize_o_maps nvidia_bugs

O

opaque_background orthoscopic overlay overlay_lines

P

pdb_conect_all pdb_discrete_chains pdb_echo_tags pdb_formal_charges pdb_hetatm_guess_valences pdb_hetatm_sort pdb_honor_model_number pdb_insertions_go_first pdb_insure_orthogonal pdb_literal_names pdb_no_end_record pdb_reformat_names_mode pdb_retain_ids pdb_standard_order pdb_truncate_residue_name pdb_unbond_cations pdb_use_ter_records pickable png_file_gamma png_screen_gamma power pqr_no_chain_id presentation presentation_auto_quit presentation_auto_start presentation_mode preserve_chempy_ids pymol_space_max_blue pymol_space_max_green pymol_space_max_red pymol_space_min_factor

R

raise_exceptions ramp_blend_nearby_colors rank_assisted_sorts ray_blend_blue ray_blend_colors ray_blend_green ray_blend_red ray_clip_shadows ray_color_ramps ray_default_renderer ray_direct_shade ray_hint_camera ray_hint_shadow ray_improve_shadows ray_interior_color ray_interior_mode ray_interior_reflect ray_interior_shadows ray_interior_texture ray_label_specular ray_legacy_lighting ray_max_passes ray_opaque_background ray_orthoscopic ray_oversample_cutoff ray_pixel_scale ray_scatter ray_shadow ray_shadow_decay_factor ray_shadow_decay_range ray_shadow_fudge ray_shadows ray_spec_local ray_texture ray_texture_settings ray_trace_color ray_trace_depth_factor ray_trace_disco_factor ray_trace_fog ray_trace_fog_start ray_trace_frames ray_trace_gain ray_trace_mode ray_trace_persist_cutoff ray_trace_slope_factor ray_trace_trans_cutoff ray_transparency_contrast ray_transparency_oblique ray_transparency_oblique_power ray_transparency_shadows ray_transparency_spec_cut ray_transparency_specular ray_triangle_fudge reflect reflect_power retain_order ribbon_color ribbon_nucleic_acid_mode ribbon_power ribbon_power_b ribbon_radius ribbon_sampling ribbon_side_chain_helper ribbon_smooth ribbon_throw ribbon_trace_atoms ribbon_width robust_logs rock rock_delay roving_byres roving_cartoon roving_delay roving_detail roving_isomesh roving_isosurface roving_labels roving_lines roving_map1_level roving_map1_name roving_map2_level roving_map2_name roving_map3_level roving_map3_name roving_nb_spheres roving_nonbonded roving_origin roving_origin_z roving_origin_z_cushion roving_polar_contacts roving_polar_cutoff roving_ribbon roving_selection roving_spheres roving_sticks

S

scene_animation scene_animation_duration scene_buttons scene_buttons_mode scene_current_name scene_loop scene_restart_movie_delay scenes_changed sculpt_angl_weight sculpt_auto_center sculpt_avd_excl sculpt_avd_gap sculpt_avd_range sculpt_avd_weight sculpt_bond_weight sculpt_field_mask sculpt_hb_overlap sculpt_hb_overlap_base sculpt_line_weight sculpt_max_max sculpt_max_min sculpt_max_scale sculpt_max_weight sculpt_memory sculpt_min_max sculpt_min_min sculpt_min_scale sculpt_min_weight sculpt_nb_interval sculpt_plan_weight sculpt_pyra_weight sculpt_tors_tolerance sculpt_tors_weight sculpt_tri_max sculpt_tri_min sculpt_tri_mode sculpt_tri_scale sculpt_tri_weight sculpt_vdw_scale sculpt_vdw_scale14 sculpt_vdw_vis_max sculpt_vdw_vis_mid sculpt_vdw_vis_min sculpt_vdw_vis_mode sculpt_vdw_weight sculpt_vdw_weight14 sculpting sculpting_cycles sdof_drag_scale secondary_structure security sel_counter selection_overlay selection_round_points selection_visible_only selection_width selection_width_max selection_width_scale seq_view seq_view_alignment seq_view_color seq_view_discrete_by_state seq_view_fill_char seq_view_fill_color seq_view_format seq_view_label_color seq_view_label_mode seq_view_label_spacing seq_view_label_start seq_view_location seq_view_overlay seq_view_unaligned_color seq_view_unaligned_mode session_cache_optimize session_changed session_compression session_file session_migration session_version_check shininess show_alpha_checker show_progress simplify_display_lists single_image slice_dynamic_grid slice_dynamic_grid_resolution slice_grid slice_height_map slice_height_scale slice_track_camera slow_idle smooth_color_triangle solvent_radius spec_count spec_direct spec_direct_power spec_power spec_reflect specular specular_intensity sphere_color sphere_mode sphere_point_max_size sphere_point_size sphere_quality sphere_scale sphere_solvent sphere_transparency spheroid_fill spheroid_scale spheroid_smooth ss_helix_phi_exclude ss_helix_phi_include ss_helix_phi_target ss_helix_psi_exclude ss_helix_psi_include ss_helix_psi_target ss_strand_phi_exclude ss_strand_phi_include ss_strand_phi_target ss_strand_psi_exclude ss_strand_psi_include ss_strand_psi_target state static_singletons stereo stereo_angle stereo_double_pump_mono stereo_mode stereo_shift stick_ball stick_ball_ratio stick_color stick_fixed_radius stick_nub stick_overlap stick_quality stick_radius stick_transparency stick_valence_scale stop_on_exceptions suppress_hidden surface_best surface_carve_cutoff surface_carve_normal_cutoff surface_carve_selection surface_carve_state surface_cavity_cutoff surface_cavity_mode surface_cavity_radius surface_circumscribe surface_clear_cutoff surface_clear_selection surface_clear_state surface_color surface_debug surface_miserable surface_mode surface_negative_color surface_negative_visible surface_normal surface_optimize_subsets surface_poor surface_proximity surface_quality surface_ramp_above_mode surface_solvent surface_trim_cutoff surface_trim_factor surface_type suspend_updates swap_dsn6_bytes sweep_angle sweep_mode sweep_phase sweep_speed

T

test1 test2 text texture_fonts trace_atoms_mode transparency transparency_global_sort transparency_mode transparency_picking_mode triangle_max_passes trim_dots two_sided_lighting

U

use_display_lists

V

valence valence_default valence_mode validate_object_names valence_size virtual_trackball

W

wildcard wizard_prompt_mode wrap_output