Difference between revisions of "Settings"

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PyMOL is incredible 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!
+
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 '''[[:Category:Settings|documented 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 '''[[:Category:Settings|documented settings]]'''.
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If you feel like documenting them, and what they do, feel free.
 
If you feel like documenting them, and what they do, feel free.
  
  active_selections             ray_default_renderer       
+
===A===
  [[all_states]]                     ray_direct_shade           
+
[[active_selections]]
  [[ambient]]                       ray_hint_camera             
+
[[all_states]]
  angle_label_position           ray_hint_shadow             
+
[[ambient]]
  angle_size                     ray_improve_shadows         
+
[[angle_color]]
  animation                     ray_interior_color         
+
[[angle_label_position]]
  animation_duration             ray_interior_mode           
+
[[angle_size]]
  [[antialias]]                     ray_interior_reflect       
+
[[animation]]
  async_builds                   ray_interior_shadows       
+
[[animation_duration]]
  [[atom_name_wildcard]]             ray_interior_texture       
+
[[antialias]]
  auto_classify_atoms           ray_legacy_lighting         
+
[[async_builds]]
  auto_color                    ray_max_passes             
+
[[ati_bugs]]
  auto_dss                      [[ray_opaque_background]]      
+
[[atom_name_wildcard]]
  auto_hide_selections          [[ray_orthoscopic]]            
+
[[auto_classify_atoms]]
  auto_indicate_flags            ray_oversample_cutoff       
+
[[auto_color]]
  auto_number_selections        ray_pixel_scale             
+
[[auto_copy_images]]
  auto_remove_hydrogens          [[ray_shadow]]                  
+
[[auto_defer_builds]]
  auto_sculpt                    ray_shadow_decay_factor     
+
[[auto_dss]]
  auto_show_lines                ray_shadow_decay_range     
+
[[auto_hide_selections]]
  auto_show_nonbonded            ray_shadow_fudge           
+
[[auto_indicate_flags]]
  auto_show_selections          [[ray_shadows]]                
+
[[auto_number_selections]]
  auto_show_spheres              ray_texture                 
+
[[auto_remove_hydrogens]]
  [[auto_zoom]]                     ray_texture_settings       
+
[[auto_rename_duplicate_objects]]
  [[backface_cull]]                 ray_trace_depth_factor     
+
[[auto_sculpt]]
  batch_prefix                  ray_trace_disco_factor     
+
[[auto_show_lines]]
  [[bg_rgb]]                         [[ray_trace_fog]]              
+
[[auto_show_nonbonded]]
  bonding_vdw_cutoff            ray_trace_fog_start         
+
[[auto_show_selections]]
  button_mode                    [[ray_trace_frames]]          
+
[[auto_show_spheres]]
  button_mode_name              ray_trace_gain             
+
[[auto_zoom]]
  cache_display                  [[Ray#Modes|ray_trace_mode]]
+
 
  cache_frames                  ray_trace_slope_factor     
+
===B===
  cache_memory                  ray_transparency_contrast   
+
[[backface_cull]]
  [[cartoon_color]]                 ray_transparency_shadows   
+
[[batch_prefix]]
  [[Cartoon Helix Settings|cartoon_cylindrical_helices]]   ray_transparency_spec_cut   
+
[[bg_rgb]]
  cartoon_debug                  ray_transparency_specular   
+
[[bonding_vdw_cutoff]]
  [[cartoon_discrete_colors]]       ray_triangle_fudge         
+
[[button_mode]]
  [[cartoon_dumbbell_length]]       [[reflect]]                    
+
[[button_mode_name]]
  [[cartoon_dumbbell_radius]]       reflect_power               
+
 
  [[cartoon_dumbbell_width]]         retain_order               
+
===C===
  [[Cartoon Helix Settings|cartoon_fancy_helices]]         [[ribbon_color]]                
+
[[cache_display]]
  [[cartoon_fancy_sheets]]           ribbon_nucleic_acid_mode   
+
[[cache_frames]]
  [[cartoon_flat_cycles]]           ribbon_power               
+
[[cache_max]]
  [[cartoon_flat_sheets]]           ribbon_power_b             
+
[[cache_memory]]
  [[Cartoon_helix_radius]]           ribbon_radius               
+
[[cache_mode]]
  [[cartoon_highlight_color]]       [[ribbon_sampling]]            
+
[[cartoon_color]]
  cartoon_ladder_color          ribbon_side_chain_helper   
+
[[cartoon_cylindrical_helices]]
  cartoon_ladder_mode            [[ribbon_smooth]]              
+
[[cartoon_debug]]
  cartoon_ladder_radius          ribbon_throw               
+
[[cartoon_discrete_colors]]
  cartoon_loop_cap              ribbon_trace_atoms         
+
[[cartoon_dumbbell_length]]
  cartoon_loop_quality          [[ribbon_width]]                
+
[[cartoon_dumbbell_radius]]
  cartoon_loop_radius            robust_logs                 
+
[[cartoon_dumbbell_width]]
  [[cartoon_nucleic_acid_color]]     rock_delay                 
+
[[cartoon_fancy_helices]]
  [[cartoon_nucleic_acid_mode]]     roving_byres               
+
[[cartoon_fancy_sheets]]
  [[cartoon_oval_length]]           roving_cartoon             
+
[[cartoon_flat_cycles]]
  [[cartoon_oval_quality]]           roving_delay               
+
[[cartoon_flat_sheets]]
  [[cartoon_oval_width]]             roving_detail               
+
[[cartoon_helix_radius]]
  cartoon_power                  roving_isomesh             
+
[[cartoon_highlight_color]]
  cartoon_power_b                roving_isosurface           
+
[[cartoon_ladder_color]]
  cartoon_putty_quality          roving_labels               
+
[[cartoon_ladder_mode]]
  cartoon_putty_radius          roving_lines               
+
[[cartoon_ladder_radius]]
  cartoon_putty_range            roving_map1_level           
+
[[cartoon_loop_cap]]
  cartoon_putty_scale_max        roving_map1_name           
+
[[cartoon_loop_quality]]
  cartoon_putty_scale_min        roving_map2_level           
+
[[cartoon_loop_radius]]
  cartoon_putty_scale_power      roving_map2_name           
+
[[cartoon_nucleic_acid_color]]
  [[cartoon_rect_length]]           roving_map3_level           
+
[[cartoon_nucleic_acid_mode]]
  [[cartoon_rect_width]]             roving_map3_name           
+
[[cartoon_oval_length]]
  cartoon_refine                roving_nb_spheres           
+
[[cartoon_oval_quality]]
  cartoon_refine_normals        roving_nonbonded           
+
[[cartoon_oval_width]]
  cartoon_refine_tips            roving_origin               
+
[[cartoon_power]]
  cartoon_ring_color            roving_origin_z             
+
[[cartoon_power_b]]
  cartoon_ring_finder            roving_origin_z_cushion     
+
[[cartoon_putty_quality]]
  [[cartoon_ring_mode]]             roving_polar_contacts       
+
[[cartoon_putty_radius]]
  cartoon_ring_radius            roving_polar_cutoff         
+
[[cartoon_putty_range]]
  [[cartoon_ring_transparency]]     roving_ribbon               
+
[[cartoon_putty_scale_max]]
  cartoon_ring_width            roving_selection           
+
[[cartoon_putty_scale_min]]
  [[cartoon_round_helices]]         roving_spheres             
+
[[cartoon_putty_scale_power]]
  [[cartoon_sampling]]               roving_sticks               
+
[[cartoon_putty_transform]]
  [[cartoon_side_chain_helper]]     scene_animation             
+
[[cartoon_rect_length]]
  cartoon_smooth_cycles          scene_animation_duration   
+
[[cartoon_rect_width]]
  cartoon_smooth_first          scene_current_name         
+
[[cartoon_refine]]
  cartoon_smooth_last            scene_loop                 
+
[[cartoon_refine_normals]]
  [[cartoon_smooth_loops]]           scene_restart_movie_delay   
+
[[cartoon_refine_tips]]
  cartoon_throw                  scenes_changed             
+
[[cartoon_ring_color]]
  cartoon_trace_atoms            sculpt_angl_weight         
+
[[cartoon_ring_finder]]
  [[cartoon_transparency]]           sculpt_auto_center         
+
[[cartoon_ring_mode]]
  cartoon_tube_cap              sculpt_avd_excl             
+
[[cartoon_ring_radius]]
  cartoon_tube_quality          sculpt_avd_gap             
+
[[cartoon_ring_transparency]]
  cartoon_tube_radius            sculpt_avd_range           
+
[[cartoon_ring_width]]
  [[cavity_cull]]                   sculpt_avd_weight           
+
[[cartoon_round_helices]]
  cgo_dot_radius                sculpt_bond_weight         
+
[[cartoon_sampling]]
  cgo_dot_width                  sculpt_field_mask           
+
[[cartoon_side_chain_helper]]
  cgo_line_radius                sculpt_hb_overlap           
+
[[cartoon_smooth_cycles]]
  cgo_line_width                sculpt_hb_overlap_base     
+
[[cartoon_smooth_first]]
  cgo_ray_width_scale            sculpt_line_weight         
+
[[cartoon_smooth_last]]
  cgo_sphere_quality            sculpt_max_max             
+
[[cartoon_smooth_loops]]
  cgo_transparency              sculpt_max_min             
+
[[cartoon_throw]]
  clamp_colors                  sculpt_max_scale           
+
[[cartoon_trace_atoms]]
  connect_bonded                sculpt_max_weight           
+
[[cartoon_transparency]]
  connect_cutoff                sculpt_memory               
+
[[cartoon_tube_cap]]
  connect_mode                  sculpt_min_max             
+
[[cartoon_tube_quality]]
  coulomb_cutoff                sculpt_min_min             
+
[[cartoon_tube_radius]]
  coulomb_dielectric            sculpt_min_scale           
+
[[cavity_cull]]
  coulomb_units_factor          sculpt_min_weight           
+
[[cgo_dot_radius]]
  cull_spheres                  sculpt_nb_interval         
+
[[cgo_dot_width]]
  [[Dash_Gap]]                       sculpt_plan_weight         
+
[[cgo_ellipsoid_quality]]
  [[Dash_Length]]                   sculpt_pyra_weight         
+
[[cgo_line_radius]]
  [[Dash_Radius]]                   sculpt_tors_tolerance       
+
[[cgo_line_width]]
  [[Dash_Round_Ends]]               sculpt_tors_weight         
+
[[cgo_ray_width_scale]]
  dash_width                    sculpt_tri_max             
+
[[cgo_sphere_quality]]
  debug_pick                    sculpt_tri_min             
+
[[cgo_transparency]]
  defer_builds_mode              sculpt_tri_mode             
+
[[clamp_colors]]
  defer_updates                  sculpt_tri_scale           
+
[[cone_quality]]
  [[depth_cue]]                     sculpt_tri_weight           
+
[[connect_bonded]]
  dihedral_label_position        sculpt_vdw_scale           
+
[[connect_cutoff]]
  dihedral_size                  sculpt_vdw_scale14         
+
[[connect_mode]]
  direct                        sculpt_vdw_vis_max         
+
[[coulomb_cutoff]]
  dist_counter                  sculpt_vdw_vis_mid         
+
[[coulomb_dielectric]]
  distance_exclusion            sculpt_vdw_vis_min         
+
[[coulomb_units_factor]]
  dot_color                      sculpt_vdw_vis_mode         
+
[[cull_spheres]]
  dot_density                    sculpt_vdw_weight           
+
[[cylinder_shader_ff_workaround]]
  dot_hydrogens                  sculpt_vdw_weight14         
+
 
  dot_lighting                  sculpting                   
+
===D===
  dot_mode                      sculpting_cycles           
+
[[dash_color]]
  dot_normals                    secondary_structure         
+
[[dash_gap]]
  [[dot_radius]]                     security                   
+
[[dash_length]]
  dot_solvent                    sel_counter
+
[[dash_radius]]
  [[dot_width]]                     selection_overlay           
+
[[dash_round_ends]]
  draw_frames                    selection_round_points     
+
[[dash_width]]
  editor_auto_dihedral          selection_visible_only     
+
[[debug_pick]]
  editor_auto_origin            [[selection_width]]            
+
[[defer_builds_mode]]
  editor_label_fragments        selection_width_max         
+
[[defer_updates]]
  fast_idle                      selection_width_scale       
+
[[depth_cue]]
  fetch_path                    [[seq_view]]                    
+
[[dihedral_color]]
  [[Field_Of_View]]                 seq_view_alignment         
+
[[dihedral_label_position]]
  fit_iterations                seq_view_color             
+
[[dihedral_size]]
  fit_tolerance                  seq_view_discrete_by_state 
+
[[direct]]
  float_labels                  seq_view_fill_char         
+
[[dist_counter]]
  [[fog]]                           seq_view_fill_color         
+
[[distance_exclusion]]
  [[fog_start]]                     seq_view_format             
+
[[dot_color]]
  frame                          seq_view_label_color       
+
[[dot_density]]
  full_screen                    seq_view_label_mode         
+
[[dot_hydrogens]]
  gamma                          seq_view_label_spacing     
+
[[dot_lighting]]
  gaussian_b_adjust              seq_view_label_start       
+
[[dot_mode]]
  gaussian_b_floor              [[seq_view_location]]          
+
[[dot_normals]]
  gaussian_resolution            seq_view_overlay           
+
[[dot_radius]]
  gl_ambient                    seq_view_unaligned_color   
+
[[dot_solvent]]
  [[grid_mode]]
+
[[dot_width]]
  [[grid_slot]]
+
[[draw_frames]]
  h_bond_cone                    seq_view_unaligned_mode     
+
 
  h_bond_cutoff_center          session_file               
+
===E===
  h_bond_cutoff_edge            session_migration           
+
[[editor_auto_dihedral]]
  h_bond_exclusion              session_version_check       
+
[[editor_auto_origin]]
  h_bond_max_angle              [[shininess]]
+
[[editor_label_fragments]]
  h_bond_power_a                show_alpha_checker         
+
[[ellipsoid_color]]
  h_bond_power_b                show_progress               
+
[[ellipsoid_probability]]
  [[half_bonds]]                     simplify_display_lists     
+
[[ellipsoid_quality]]
  [[hash_max]]                       single_image               
+
[[ellipsoid_scale]]
  hide_underscore_names          slice_dynamic_grid         
+
[[ellipsoid_transparency]]
  idle_delay                    slice_dynamic_grid_resolution
+
 
  ignore_case                    slice_grid                 
+
===F===
  ignore_pdb_segi                slice_height_map           
+
[[fast_idle]]
  image_dots_per_inch            slice_height_scale         
+
[[fetch_path]]
  internal_feedback              slice_track_camera         
+
[[field_of_view]]
  [[Internal Gui|internal_gui]]                   slow_idle                   
+
[[fit_iterations]]
  internal_gui_control_size      smooth_color_triangle       
+
[[fit_tolerance]]
  internal_gui_mode              solvent_radius             
+
[[float_labels]]
  internal_gui_width            spec_count                 
+
[[fog]]
  [[internal_prompt]]               spec_direct                 
+
[[fog_start]]
  isomesh_auto_state            spec_direct_power           
+
[[frame]]
  [[label_color]]                   spec_power                 
+
[[full_screen]]
  [[Label_font_id]]                 [[spec_reflect]]                
+
 
  [[Label_outline_color]]           specular                   
+
===G===
  [[label_position]]                 specular_intensity         
+
[[gamma]]
  [[label_shadow_mode]]             [[sphere_color]]                
+
[[gaussian_b_adjust]]
  [[label_size]]                     [[sphere_mode]]                
+
[[gaussian_b_floor]]
  legacy_mouse_zoom              sphere_point_max_size       
+
[[gaussian_resolution]]
  legacy_vdw_radii              sphere_point_size           
+
[[geometry_export_mode]]
  light                          [[sphere_quality]]              
+
[[gl_ambient]]
  light2                        [[sphere_scale]]                
+
[[gradient_max_length]]
  light3                        sphere_solvent             
+
[[gradient_min_length]]
  light4                        [[sphere_transparency]]        
+
[[gradient_min_slope]]
  light5                        spheroid_fill               
+
[[gradient_normal_min_dot]]
  light6                        spheroid_scale             
+
[[gradient_spacing]]
  light7                        spheroid_smooth             
+
[[gradient_step_size]]
  light8                        ss_helix_phi_exclude       
+
[[gradient_symmetry]]
  light9                        ss_helix_phi_include       
+
[[grid_max]]
  [[light_count]]                   ss_helix_phi_target         
+
[[grid_mode]]
  line_radius                    ss_helix_psi_exclude       
+
[[grid_slot]]
  [[line_smooth]]                   ss_helix_psi_include       
+
[[group_arrow_prefix]]
  line_stick_helper              ss_helix_psi_target         
+
[[group_auto_mode]]
  line_width                    ss_strand_phi_exclude       
+
[[group_full_member_names]]
  log_box_selections            ss_strand_phi_include       
+
 
  log_conformations              ss_strand_phi_target       
+
===H===
  logging                        ss_strand_psi_exclude       
+
[[h_bond_cone]]
  matrix_mode                    ss_strand_psi_include       
+
[[h_bond_cutoff_center]]
  max_threads                    ss_strand_psi_target       
+
[[h_bond_cutoff_edge]]
  max_triangles                  state                       
+
[[h_bond_exclusion]]
  [[mesh_color]]                     static_singletons           
+
[[h_bond_from_proton]]
  [[mesh_lighting]]                 [[stereo]]
+
[[h_bond_max_angle]]
  [[mesh_mode]]                     [[stereo_angle]]
+
[[h_bond_power_a]]
  mesh_normals                  stereo_double_pump_mono     
+
[[h_bond_power_b]]
  [[mesh_quality]]                   [[stereo_mode]]                
+
[[half_bonds]]
  mesh_radius                    stereo_shift               
+
[[hash_max]]
  mesh_solvent                  [[stick_ball]]                  
+
[[hide_long_bonds]]
  [[mesh_type]]                     [[stick_ball_ratio]]            
+
[[hide_underscore_names]]
  [[mesh_width]]                     [[stick_color]]
+
 
  [[min_mesh_spacing]]               stick_fixed_radius         
+
===I===
  mouse_limit                    [[stick_nub]]                  
+
[[idle_delay]]
  mouse_restart_movie_delay      stick_overlap               
+
[[ignore_case]]
  mouse_scale                    stick_quality               
+
[[ignore_pdb_segi]]
  mouse_selection_mode          stick_radius               
+
[[image_copy_always]]
  movie_delay                    [[stick_transparency]]          
+
[[image_dots_per_inch]]
  movie_loop                    stick_valence_scale         
+
[[internal_feedback]]
  multiplex                      stop_on_exceptions         
+
[[internal_gui]]
  no_idle                        surface_best               
+
[[internal_gui_control_size]]
  nonbonded_size                surface_carve_cutoff       
+
[[internal_gui_mode]]
  normal_workaround              surface_carve_selection     
+
[[internal_gui_width]]
  normalize_ccp4_maps            surface_carve_state         
+
[[internal_prompt]]
  normalize_grd_maps            surface_circumscribe       
+
[[isomesh_auto_state]]
  normalize_o_maps              surface_clear_cutoff       
+
 
  nvidia_bugs                    surface_clear_selection     
+
===J===
  opaque_background              surface_clear_state         
+
 
  [[orthoscopic]]                   surface_color               
+
===K===
  overlay                        surface_debug               
+
 
  overlay_lines                  surface_miserable           
+
===L===
  pdb_conect_all                surface_mode               
+
[[label_angle_digits]]
  pdb_discrete_chains            surface_normal             
+
[[label_color]]
  pdb_echo_tags                  surface_optimize_subsets   
+
[[label_digits]]
  pdb_hetatm_sort                surface_poor               
+
[[label_dihedral_digits]]
  pdb_honor_model_number        surface_proximity           
+
[[label_distance_digits]]
  pdb_insertions_go_first        surface_quality             
+
[[label_font_id]]
  pdb_insure_orthogonal          surface_ramp_above_mode     
+
[[label_outline_color]]
  pdb_literal_names              surface_solvent             
+
[[label_position]]
  pdb_no_end_record              surface_trim_cutoff         
+
[[label_shadow_mode]]
  pdb_reformat_names_mode        surface_trim_factor         
+
[[label_size]]
  pdb_retain_ids                surface_type               
+
[[legacy_mouse_zoom]]
  pdb_standard_order            suspend_updates             
+
[[legacy_vdw_radii]]
  pdb_truncate_residue_name      swap_dsn6_bytes             
+
[[light]]
  pdb_unbond_cations            sweep_angle                 
+
[[light2]]
  pdb_use_ter_records            sweep_mode                 
+
[[light3]]
  [[pickable]]                       sweep_phase                 
+
[[light4]]
  png_file_gamma                sweep_speed                 
+
[[light5]]
  png_screen_gamma              test1                       
+
[[light6]]
  power                          test2                       
+
[[light7]]
  pqr_no_chain_id                text                       
+
[[light8]]
  presentation                  texture_fonts               
+
[[light9]]
  presentation_auto_quit        [[transparency]]                
+
[[light_count]]
  presentation_auto_start        transparency_mode           
+
[[line_color]]
  presentation_mode              transparency_picking_mode   
+
[[line_radius]]
  preserve_chempy_ids            triangle_max_passes         
+
[[line_smooth]]
  pymol_space_max_blue          trim_dots                   
+
[[line_stick_helper]]
  pymol_space_max_green          [[two_sided_lighting]]
+
[[line_width]]
  pymol_space_max_red            use_display_lists           
+
[[log_box_selections]]
  pymol_space_min_factor        [[valence]]                     
+
[[log_conformations]]
  raise_exceptions              valence_default             
+
[[logging]]
  rank_assisted_sorts            valence_size               
+
 
  ray_blend_blue                validate_object_names       
+
===M===
  ray_blend_colors              [[virtual_trackball]]           
+
[[map_auto_expand_sym]]
  ray_blend_green                wildcard                   
+
[[matrix_mode]]
  ray_blend_red                  wizard_prompt_mode         
+
[[max_threads]]
  ray_color_ramps                wrap_output                 
+
[[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]]
 +
 
 +
===Q===
 +
 
 +
===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|valence_mode]]
 +
[[validate_object_names]]
 +
[[valence|valence_size]]
 +
[[virtual_trackball]]
 +
 
 +
===W===
 +
[[wildcard]]
 +
[[wizard_prompt_mode]]
 +
[[wrap_output]]
 +
 
 +
===X===
 +
 
 +
===Y===
 +
 
 +
===Z===
  
 
[[Category:Settings|All Settings]]
 
[[Category:Settings|All Settings]]

Latest revision as of 06:53, 6 June 2014

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

J

K

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

Q

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

X

Y

Z