https://wiki.pymol.org/api.php?action=feedcontributions&feedformat=atom&user=TheSmell PyMOL Wiki - User contributions [en] 2026-05-07T04:03:54Z User contributions MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Settings&diff=10135 Settings 2006-12-19T14:08:27Z <p>TheSmell: </p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> [[ambient]] ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] [[reflect]] <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> [[cavity_cull]] sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> [[fog]] seq_view_fill_color <br /> [[fog_start]] seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle [[shininess]]<br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> [[label_position]] specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 [[sphere_transparency]] <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> [[light_count]] ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> [[mesh_color]] static_singletons <br /> [[mesh_lighting]] stereo <br /> [[mesh_mode]] stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> [[mesh_quality]] stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> [[mesh_type]] [[stick_ball_ratio]] <br /> [[mesh_width]] stick_color <br /> [[min_mesh_spacing]] stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors [[virtual_trackball]] <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=Virtual_trackball&diff=10614 Virtual trackball 2006-12-19T14:08:02Z <p>TheSmell: Created new settings page for virtual_trackball</p> <hr /> <div>== Overview ==<br /> <br /> set virtual_trackball allows you to toggle on or off the virtual trackball feature<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set virtual_trackball, off<br /> set virtual_trackball, 0 #off<br /> <br /> set virtual_trackball, on<br /> set virtual_trackball, 1 #on<br /> &lt;/source&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10132 Settings 2006-12-04T17:21:42Z <p>TheSmell: Added Sphere transparency link</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> [[ambient]] ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] [[reflect]] <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> [[cavity_cull]] sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> [[fog]] seq_view_fill_color <br /> [[fog_start]] seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 [[sphere_transparency]] <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> [[light_count]] ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> [[mesh_color]] static_singletons <br /> [[mesh_lighting]] stereo <br /> [[mesh_mode]] stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> [[mesh_quality]] stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> [[mesh_type]] [[stick_ball_ratio]] <br /> [[mesh_width]] stick_color <br /> [[min_mesh_spacing]] stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=Sphere_transparency&diff=8928 Sphere transparency 2006-12-04T17:20:52Z <p>TheSmell: Added Sphere transparency setting</p> <hr /> <div>set sphere_transparency is used to adjust the transparency of spheres!<br /> <br /> set sphere_transparency, 0.5<br /> <br /> or<br /> <br /> set sphere_transparency=0.5, selection<br /> <br /> Where 1.0 is invisible and 0.0 completely solid</div> TheSmell https://wiki.pymol.org/index.php?title=Fog&diff=7354 Fog 2006-12-04T15:03:25Z <p>TheSmell: </p> <hr /> <div>== Overview ==<br /> <br /> set fog allows Depth Cue (or fog!) to be turned on or off in the interactive viewer, not for ray traced images, for this see [[Ray_Trace_Fog]]<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set fog, off<br /> set fog, 0 #off<br /> <br /> set fog, on<br /> set fog, 1 #on<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:fog_on.png|fog on<br /> Image:fog_off.png|fog off<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=Fog&diff=7353 Fog 2006-12-04T15:03:01Z <p>TheSmell: added link to ray_trace_fog</p> <hr /> <div>== Overview ==<br /> <br /> set fog allows Depth Cue (or fog!) to be turned on or off in the interactive viewer, not for ray traced images, for this see [[ray_trace_fog]]<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set fog, off<br /> set fog, 0 #off<br /> <br /> set fog, on<br /> set fog, 1 #on<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:fog_on.png|fog on<br /> Image:fog_off.png|fog off<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10131 Settings 2006-11-28T15:29:01Z <p>TheSmell: Added links</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> [[ambient]] ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] [[reflect]] <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> [[cavity_cull]] sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> [[fog]] seq_view_fill_color <br /> [[fog_start]] seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> [[light_count]] ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> [[mesh_color]] static_singletons <br /> [[mesh_lighting]] stereo <br /> [[mesh_mode]] stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> [[mesh_quality]] stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> [[mesh_type]] [[stick_ball_ratio]] <br /> [[mesh_width]] stick_color <br /> [[min_mesh_spacing]] stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=Reflect&diff=10039 Reflect 2006-11-28T15:27:47Z <p>TheSmell: Created new settings page for reflect</p> <hr /> <div>== Overview ==<br /> <br /> set reflect controls the amount of light reflection and the effect directional light therefore has on shadows and the general lighting of the scene.<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set reflect, &lt;number&gt; #default 0.5<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:reflect_minus1.png|reflect -1<br /> Image:refelect_0.png|reflect 0<br /> Image:reflect_0.5.png|reflect 0.5 (default)<br /> Image:refelect_1.png|reflect 1<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=File:Reflect_minus1.png&diff=2008 File:Reflect minus1.png 2006-11-28T15:25:21Z <p>TheSmell: Image for pymol wiki settings illustarting the reflect setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the reflect setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=File:Reflect_0.5.png&diff=2493 File:Reflect 0.5.png 2006-11-28T15:25:08Z <p>TheSmell: Image for pymol wiki settings illustarting the reflect setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the reflect setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=File:Refelect_1.png&diff=2250 File:Refelect 1.png 2006-11-28T15:24:48Z <p>TheSmell: Image for pymol wiki settings illustarting the reflect setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the reflect setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=File:Refelect_0.png&diff=2006 File:Refelect 0.png 2006-11-28T15:24:34Z <p>TheSmell: Image for pymol wiki settings illustarting the reflect setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the reflect setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=Light_count&diff=12713 Light count 2006-11-28T14:58:43Z <p>TheSmell: Created new settings page for light_count</p> <hr /> <div>== Overview ==<br /> <br /> set light_count definies the number of light sources.&lt;br&gt;<br /> Setting to 0 or 1 removes any directional light source resulting in no shadows. Light_count does affect [[ambient]] lighting.<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set light_count, &lt;integer&gt; #default 2<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:light_count_0.png|light_count 0<br /> Image:light_count_2.png|light_count 2 (default)<br /> Image:light_count_10.png|light_count 10<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=File:Light_count_10.png&diff=2126 File:Light count 10.png 2006-11-28T14:56:28Z <p>TheSmell: Image for pymol wiki settings illustarting the light_count setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the light_count setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=File:Light_count_2.png&diff=2370 File:Light count 2.png 2006-11-28T14:56:14Z <p>TheSmell: Image for pymol wiki settings illustarting the light_count setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the light_count setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=File:Light_count_0.png&diff=1872 File:Light count 0.png 2006-11-28T14:56:00Z <p>TheSmell: Image for pymol wiki settings illustarting the light_count setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the light_count setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10130 Settings 2006-11-28T11:56:37Z <p>TheSmell: Added link to cavity_cull</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> [[ambient]] ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] reflect <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> [[cavity_cull]] sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> [[fog]] seq_view_fill_color <br /> [[fog_start]] seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> [[mesh_color]] static_singletons <br /> [[mesh_lighting]] stereo <br /> [[mesh_mode]] stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> [[mesh_quality]] stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> [[mesh_type]] [[stick_ball_ratio]] <br /> [[mesh_width]] stick_color <br /> [[min_mesh_spacing]] stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=Cavity_cull&diff=5025 Cavity cull 2006-11-28T11:53:35Z <p>TheSmell: Created new settings page for cavity_cull</p> <hr /> <div>== Overview ==<br /> <br /> set cavity_cull allows the user to define how sensitive pymol it to detecting cavities within the interior of a molecule.&lt;br&gt;<br /> Smaller cavities are not detected as the cavity cull value is increased. The value ''may'' correspond in angstroms a dimension of the cavity approximately.<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set cavity_cull, &lt;number&gt; #default 2<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:cavity_0.jpg|cavity_cull 0<br /> Image:cavity_default.jpg|cavity_cull 2 (default)<br /> Image:cavity_20.jpg|cavity_cull 20<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=File:Cavity_20.jpg&diff=1191 File:Cavity 20.jpg 2006-11-28T11:52:01Z <p>TheSmell: Image for pymol wiki settings illustarting the cavity_cull setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the cavity_cull setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=File:Cavity_default.jpg&diff=1432 File:Cavity default.jpg 2006-11-28T11:51:42Z <p>TheSmell: Image for pymol wiki settings illustarting the cavity_cull setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the cavity_cull setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=File:Cavity_0.jpg&diff=1677 File:Cavity 0.jpg 2006-11-28T11:51:16Z <p>TheSmell: Image for pymol wiki settings illustarting the cavity_cull setting Created using pymol 0.99 and pdb file 1j84</p> <hr /> <div>Image for pymol wiki settings illustarting the cavity_cull setting Created using pymol 0.99 and pdb file 1j84</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10129 Settings 2006-11-27T18:59:14Z <p>TheSmell: Added link to mesh_width</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> [[ambient]] ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] reflect <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> [[fog]] seq_view_fill_color <br /> [[fog_start]] seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> [[mesh_color]] static_singletons <br /> [[mesh_lighting]] stereo <br /> [[mesh_mode]] stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> [[mesh_quality]] stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> [[mesh_type]] [[stick_ball_ratio]] <br /> [[mesh_width]] stick_color <br /> [[min_mesh_spacing]] stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=Mesh_width&diff=6968 Mesh width 2006-11-27T18:58:09Z <p>TheSmell: Created new settings page for mesh_width</p> <hr /> <div>== Overview ==<br /> <br /> set mesh_width adjusts the thickness of the mesh lines<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set mesh_width, &lt;number&gt; #default 0.5<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:min_mesh_spacing_default.jpg|mesh_width 0.5 (default)<br /> Image:mesh_width_3.jpg|mesh_width 3<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=File:Mesh_width_3.jpg&diff=2148 File:Mesh width 3.jpg 2006-11-27T18:57:52Z <p>TheSmell: Image for pymol wiki settings illustarting the mesh_width setting Created using pymol 0.99 and pdb file 1aiw</p> <hr /> <div>Image for pymol wiki settings illustarting the mesh_width setting Created using pymol 0.99 and pdb file 1aiw</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10128 Settings 2006-11-27T18:48:11Z <p>TheSmell: Added link to some mesh settings</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> [[ambient]] ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] reflect <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> [[fog]] seq_view_fill_color <br /> [[fog_start]] seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> [[mesh_color]] static_singletons <br /> [[mesh_lighting]] stereo <br /> [[mesh_mode]] stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> [[mesh_quality]] stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> [[mesh_type]] [[stick_ball_ratio]] <br /> mesh_width stick_color <br /> [[min_mesh_spacing]] stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=File:Mesh_type_1_ray.jpg&diff=2386 File:Mesh type 1 ray.jpg 2006-11-27T18:44:27Z <p>TheSmell: Image for pymol wiki settings illustarting the mesh_type setting Created using pymol 0.99 and pdb file 1aiw</p> <hr /> <div>Image for pymol wiki settings illustarting the mesh_type setting Created using pymol 0.99 and pdb file 1aiw</div> TheSmell https://wiki.pymol.org/index.php?title=File:Mesh_type_1.png&diff=2146 File:Mesh type 1.png 2006-11-27T18:43:16Z <p>TheSmell: Image for pymol wiki settings illustarting the mesh_type setting Created using pymol 0.99 and pdb file 1aiw</p> <hr /> <div>Image for pymol wiki settings illustarting the mesh_type setting Created using pymol 0.99 and pdb file 1aiw</div> TheSmell https://wiki.pymol.org/index.php?title=File:Mesh_quality_0.jpg&diff=1886 File:Mesh quality 0.jpg 2006-11-27T18:33:05Z <p>TheSmell: Image for pymol wiki settings illustarting the mesh_quality setting Created using pymol 0.99 and pdb file 1aiw</p> <hr /> <div>Image for pymol wiki settings illustarting the mesh_quality setting Created using pymol 0.99 and pdb file 1aiw</div> TheSmell https://wiki.pymol.org/index.php?title=File:Mesh_quality_1.jpg&diff=2144 File:Mesh quality 1.jpg 2006-11-27T18:32:35Z <p>TheSmell: Image for pymol wiki settings illustarting the mesh_quality setting Created using pymol 0.99 and pdb file 1aiw</p> <hr /> <div>Image for pymol wiki settings illustarting the mesh_quality setting Created using pymol 0.99 and pdb file 1aiw</div> TheSmell https://wiki.pymol.org/index.php?title=Min_mesh_spacing&diff=6971 Min mesh spacing 2006-11-27T18:21:57Z <p>TheSmell: Created new settings page for min_mesh_spacing</p> <hr /> <div>== Overview ==<br /> <br /> set min_mesh_spacing alters spacing between mesh lines<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set min_mesh_spacing, &lt;number&gt; #default 0.6<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:min_mesh_spacing_default.jpg|min_mesh_spacing 0.6 (default)<br /> Image:min_mesh_spacing_2.jpg|min_mesh_spacing 2<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=File:Min_mesh_spacing_2.jpg&diff=1892 File:Min mesh spacing 2.jpg 2006-11-27T18:21:31Z <p>TheSmell: Image for pymol wiki settings illustarting the min_mesh_spacing setting Created using pymol 0.99 and pdb file 1aiw</p> <hr /> <div>Image for pymol wiki settings illustarting the min_mesh_spacing setting Created using pymol 0.99 and pdb file 1aiw</div> TheSmell https://wiki.pymol.org/index.php?title=File:Min_mesh_spacing_default.jpg&diff=2150 File:Min mesh spacing default.jpg 2006-11-27T18:21:01Z <p>TheSmell: Image for pymol wiki settings illustarting the min_mesh_spacing setting Created using pymol 0.99 and pdb file 1aiw</p> <hr /> <div>Image for pymol wiki settings illustarting the min_mesh_spacing setting Created using pymol 0.99 and pdb file 1aiw</div> TheSmell https://wiki.pymol.org/index.php?title=Mesh_mode&diff=6963 Mesh mode 2006-11-27T18:10:51Z <p>TheSmell: Created new settings page for mesh_mode</p> <hr /> <div>== Overview ==<br /> <br /> set mesh_mode is not supported as of version 0.99rc6, altering this setting has no obvious effect!<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set mesh_mode, &lt;integer&gt; #default 1<br /> &lt;/source&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10127 Settings 2006-11-27T17:27:08Z <p>TheSmell: Added link to ambient</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> [[ambient]] ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] reflect <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> [[fog]] seq_view_fill_color <br /> [[fog_start]] seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> mesh_type [[stick_ball_ratio]] <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=Ambient&diff=6325 Ambient 2006-11-27T17:25:53Z <p>TheSmell: Created new settings page for ambient</p> <hr /> <div>== Overview ==<br /> <br /> set ambient controls the amount of ambient light<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set ambient, &lt;number&gt; #default 0.1<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:ambient_minus0.4.png|ambient -0.4<br /> Image:ambient_default.png|ambient 0.1 (default)<br /> Image:ambient_0.6.png|ambient 0.6<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=File:Ambient_minus0.4.png&diff=1616 File:Ambient minus0.4.png 2006-11-27T17:24:53Z <p>TheSmell: </p> <hr /> <div></div> TheSmell https://wiki.pymol.org/index.php?title=File:Ambient_0.6.png&diff=1129 File:Ambient 0.6.png 2006-11-27T17:24:43Z <p>TheSmell: Image for pymol wiki settings illustarting the ambient setting Created using pymol 0.99 and pdb file 1bgo</p> <hr /> <div>Image for pymol wiki settings illustarting the ambient setting Created using pymol 0.99 and pdb file 1bgo</div> TheSmell https://wiki.pymol.org/index.php?title=File:Ambient_default.png&diff=1369 File:Ambient default.png 2006-11-27T17:24:33Z <p>TheSmell: Image for pymol wiki settings illustarting the ambient setting Created using pymol 0.99 and pdb file 1bgo</p> <hr /> <div>Image for pymol wiki settings illustarting the ambient setting Created using pymol 0.99 and pdb file 1bgo</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10126 Settings 2006-11-27T17:16:04Z <p>TheSmell: Added link to fog settings</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] reflect <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> [[fog]] seq_view_fill_color <br /> [[fog_start]] seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> mesh_type [[stick_ball_ratio]] <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=File:Fog_start_minus0.5.png&diff=2065 File:Fog start minus0.5.png 2006-11-27T17:12:58Z <p>TheSmell: Image for pymol wiki settings illustarting the fog_start setting Created using pymol 0.99 and pdb file 1bgo</p> <hr /> <div>Image for pymol wiki settings illustarting the fog_start setting Created using pymol 0.99 and pdb file 1bgo</div> TheSmell https://wiki.pymol.org/index.php?title=File:Fog_start_default.png&diff=1814 File:Fog start default.png 2006-11-27T17:12:47Z <p>TheSmell: Image for pymol wiki settings illustarting the fog_start setting Created using pymol 0.99 and pdb file 1bgo</p> <hr /> <div>Image for pymol wiki settings illustarting the fog_start setting Created using pymol 0.99 and pdb file 1bgo</div> TheSmell https://wiki.pymol.org/index.php?title=File:Fog_start_1.png&diff=2312 File:Fog start 1.png 2006-11-27T17:12:22Z <p>TheSmell: Image for pymol wiki settings illustarting the fog_start setting Created using pymol 0.99 and pdb file 1bgo</p> <hr /> <div>Image for pymol wiki settings illustarting the fog_start setting Created using pymol 0.99 and pdb file 1bgo</div> TheSmell https://wiki.pymol.org/index.php?title=Fog&diff=7352 Fog 2006-11-27T16:45:17Z <p>TheSmell: Created new settings page for fog</p> <hr /> <div>== Overview ==<br /> <br /> set fog allows Depth Cue (or fog!) to be turned on or off<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set fog, off<br /> set fog, 0 #off<br /> <br /> set fog, on<br /> set fog, 1 #on<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:fog_on.png|fog on<br /> Image:fog_off.png|fog off<br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=File:Fog_off.png&diff=1812 File:Fog off.png 2006-11-27T16:43:16Z <p>TheSmell: Image for pymol wiki settings illustarting the fog setting Created using pymol 0.99 and pdb file 1bgo</p> <hr /> <div>Image for pymol wiki settings illustarting the fog setting Created using pymol 0.99 and pdb file 1bgo</div> TheSmell https://wiki.pymol.org/index.php?title=File:Fog_on.png&diff=2063 File:Fog on.png 2006-11-27T16:41:54Z <p>TheSmell: Image for pymol wiki settings illustarting the fog setting Created using pymol 0.99 and pdb file 1bgo</p> <hr /> <div>Image for pymol wiki settings illustarting the fog setting Created using pymol 0.99 and pdb file 1bgo</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10125 Settings 2006-11-27T16:24:28Z <p>TheSmell: Added link to cartoon_sidechain_helper</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] reflect <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> [[cartoon_side_chain_helper]] scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> mesh_type [[stick_ball_ratio]] <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=Settings&diff=10124 Settings 2006-11-27T16:09:05Z <p>TheSmell: Added links to cartoon_rect settings</p> <hr /> <div>These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 42 done, 476 to go !<br /> <br /> active_selections ray_default_renderer <br /> [[all_states]] ray_direct_shade <br /> ambient ray_hint_camera <br /> angle_label_position ray_hint_shadow <br /> angle_size ray_improve_shadows <br /> animation ray_interior_color <br /> animation_duration ray_interior_mode <br /> [[antialias]] ray_interior_reflect <br /> async_builds ray_interior_shadows <br /> atom_name_wildcard ray_interior_texture <br /> auto_classify_atoms ray_legacy_lighting <br /> auto_color ray_max_passes <br /> auto_dss [[ray_opaque_background]] <br /> auto_hide_selections [[ray_orthoscopic]] <br /> auto_indicate_flags ray_oversample_cutoff <br /> auto_number_selections ray_pixel_scale <br /> auto_remove_hydrogens [[ray_shadow]] <br /> auto_sculpt ray_shadow_decay_factor <br /> auto_show_lines ray_shadow_decay_range <br /> auto_show_nonbonded ray_shadow_fudge <br /> auto_show_selections [[ray_shadows]] <br /> auto_show_spheres ray_texture <br /> [[auto_zoom]] ray_texture_settings <br /> [[backface_cull]] ray_trace_depth_factor <br /> batch_prefix ray_trace_disco_factor <br /> [[bg_rgb]] [[ray_trace_fog]] <br /> bonding_vdw_cutoff ray_trace_fog_start <br /> button_mode [[ray_trace_frames]] <br /> button_mode_name ray_trace_gain <br /> cache_display ray_trace_mode <br /> cache_frames ray_trace_slope_factor <br /> cache_memory ray_transparency_contrast <br /> [[cartoon_color]] ray_transparency_shadows <br /> [[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br /> cartoon_debug ray_transparency_specular <br /> [[cartoon_discrete_colors]] ray_triangle_fudge <br /> [[cartoon_dumbbell_length]] reflect <br /> [[cartoon_dumbbell_radius]] reflect_power <br /> [[cartoon_dumbbell_width]] retain_order <br /> [[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br /> [[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br /> [[cartoon_flat_cycles]] ribbon_power <br /> [[cartoon_flat_sheets]] ribbon_power_b <br /> [[Cartoon_helix_radius]] ribbon_radius <br /> [[cartoon_highlight_color]] [[ribbon_sampling]] <br /> cartoon_ladder_color ribbon_side_chain_helper <br /> cartoon_ladder_mode ribbon_smooth <br /> cartoon_ladder_radius ribbon_throw <br /> cartoon_loop_cap ribbon_trace_atoms <br /> cartoon_loop_quality [[ribbon_width]] <br /> cartoon_loop_radius robust_logs <br /> [[cartoon_nucleic_acid_color]] rock_delay <br /> [[cartoon_nucleic_acid_mode]] roving_byres <br /> [[cartoon_oval_length]] roving_cartoon <br /> [[cartoon_oval_quality]] roving_delay <br /> [[cartoon_oval_width]] roving_detail <br /> cartoon_power roving_isomesh <br /> cartoon_power_b roving_isosurface <br /> cartoon_putty_quality roving_labels <br /> cartoon_putty_radius roving_lines <br /> cartoon_putty_range roving_map1_level <br /> cartoon_putty_scale_max roving_map1_name <br /> cartoon_putty_scale_min roving_map2_level <br /> cartoon_putty_scale_power roving_map2_name <br /> [[cartoon_rect_length]] roving_map3_level <br /> [[cartoon_rect_width]] roving_map3_name <br /> cartoon_refine roving_nb_spheres <br /> cartoon_refine_normals roving_nonbonded <br /> cartoon_refine_tips roving_origin <br /> cartoon_ring_color roving_origin_z <br /> cartoon_ring_finder roving_origin_z_cushion <br /> [[cartoon_ring_mode]] roving_polar_contacts <br /> cartoon_ring_radius roving_polar_cutoff <br /> [[cartoon_ring_transparency]] roving_ribbon <br /> cartoon_ring_width roving_selection <br /> [[cartoon_round_helices]] roving_spheres <br /> [[cartoon_sampling]] roving_sticks <br /> cartoon_side_chain_helper scene_animation <br /> cartoon_smooth_cycles scene_animation_duration <br /> cartoon_smooth_first scene_current_name <br /> cartoon_smooth_last scene_loop <br /> [[cartoon_smooth_loops]] scene_restart_movie_delay <br /> cartoon_throw scenes_changed <br /> cartoon_trace_atoms sculpt_angl_weight <br /> [[cartoon_transparency]] sculpt_auto_center <br /> cartoon_tube_cap sculpt_avd_excl <br /> cartoon_tube_quality sculpt_avd_gap <br /> cartoon_tube_radius sculpt_avd_range <br /> cavity_cull sculpt_avd_weight <br /> cgo_dot_radius sculpt_bond_weight <br /> cgo_dot_width sculpt_field_mask <br /> cgo_line_radius sculpt_hb_overlap <br /> cgo_line_width sculpt_hb_overlap_base <br /> cgo_ray_width_scale sculpt_line_weight <br /> cgo_sphere_quality sculpt_max_max <br /> cgo_transparency sculpt_max_min <br /> clamp_colors sculpt_max_scale <br /> connect_bonded sculpt_max_weight <br /> connect_cutoff sculpt_memory <br /> connect_mode sculpt_min_max <br /> coulomb_cutoff sculpt_min_min <br /> coulomb_dielectric sculpt_min_scale <br /> coulomb_units_factor sculpt_min_weight <br /> cull_spheres sculpt_nb_interval <br /> [[Dash_Gap]] sculpt_plan_weight <br /> [[Dash_Length]] sculpt_pyra_weight <br /> [[Dash_Radius]] sculpt_tors_tolerance <br /> [[Dash_Round_Ends]] sculpt_tors_weight <br /> dash_width sculpt_tri_max <br /> debug_pick sculpt_tri_min <br /> defer_builds_mode sculpt_tri_mode <br /> defer_updates sculpt_tri_scale <br /> depth_cue sculpt_tri_weight <br /> dihedral_label_position sculpt_vdw_scale <br /> dihedral_size sculpt_vdw_scale14 <br /> direct sculpt_vdw_vis_max <br /> dist_counter sculpt_vdw_vis_mid <br /> distance_exclusion sculpt_vdw_vis_min <br /> dot_color sculpt_vdw_vis_mode <br /> dot_density sculpt_vdw_weight <br /> dot_hydrogens sculpt_vdw_weight14 <br /> dot_lighting sculpting <br /> dot_mode sculpting_cycles <br /> dot_normals secondary_structure <br /> dot_radius security <br /> dot_solvent sel_counter<br /> [[dot_width]] selection_overlay <br /> draw_frames selection_round_points <br /> editor_auto_dihedral selection_visible_only <br /> editor_auto_origin [[selection_width]] <br /> editor_label_fragments selection_width_max <br /> fast_idle selection_width_scale <br /> fetch_path [[seq_view]] <br /> [[Field_Of_View]] seq_view_alignment <br /> fit_iterations seq_view_color <br /> fit_tolerance seq_view_discrete_by_state <br /> float_labels seq_view_fill_char <br /> fog seq_view_fill_color <br /> fog_start seq_view_format <br /> frame seq_view_label_color <br /> full_screen seq_view_label_mode <br /> gamma seq_view_label_spacing <br /> gaussian_b_adjust seq_view_label_start <br /> gaussian_b_floor [[seq_view_location]] <br /> gaussian_resolution seq_view_overlay <br /> gl_ambient seq_view_unaligned_color <br /> h_bond_cone seq_view_unaligned_mode <br /> h_bond_cutoff_center session_file <br /> h_bond_cutoff_edge session_migration <br /> h_bond_exclusion session_version_check <br /> h_bond_max_angle shininess <br /> h_bond_power_a show_alpha_checker <br /> h_bond_power_b show_progress <br /> [[half_bonds]] simplify_display_lists <br /> hash_max single_image <br /> hide_underscore_names slice_dynamic_grid <br /> idle_delay slice_dynamic_grid_resolution<br /> ignore_case slice_grid <br /> ignore_pdb_segi slice_height_map <br /> image_dots_per_inch slice_height_scale <br /> internal_feedback slice_track_camera <br /> [[Internal Gui|internal_gui]] slow_idle <br /> internal_gui_control_size smooth_color_triangle <br /> internal_gui_mode solvent_radius <br /> internal_gui_width spec_count <br /> [[internal_prompt]] spec_direct <br /> isomesh_auto_state spec_direct_power <br /> [[label_color]] spec_power <br /> [[Label_font_id]] [[spec_reflect]] <br /> [[Label_outline_color]] specular <br /> label_position specular_intensity <br /> [[label_shadow_mode]] [[sphere_color]] <br /> [[label_size]] sphere_mode <br /> legacy_mouse_zoom sphere_point_max_size <br /> legacy_vdw_radii sphere_point_size <br /> light sphere_quality <br /> light2 [[sphere_scale]] <br /> light3 sphere_solvent <br /> light4 sphere_transparency <br /> light5 spheroid_fill <br /> light6 spheroid_scale <br /> light7 spheroid_smooth <br /> light8 ss_helix_phi_exclude <br /> light9 ss_helix_phi_include <br /> light_count ss_helix_phi_target <br /> line_radius ss_helix_psi_exclude <br /> [[line_smooth]] ss_helix_psi_include <br /> line_stick_helper ss_helix_psi_target <br /> line_width ss_strand_phi_exclude <br /> log_box_selections ss_strand_phi_include <br /> log_conformations ss_strand_phi_target <br /> logging ss_strand_psi_exclude <br /> matrix_mode ss_strand_psi_include <br /> max_threads ss_strand_psi_target <br /> max_triangles state <br /> mesh_color static_singletons <br /> mesh_lighting stereo <br /> mesh_mode stereo_angle <br /> mesh_normals stereo_double_pump_mono <br /> mesh_quality stereo_mode <br /> mesh_radius stereo_shift <br /> mesh_solvent [[stick_ball]] <br /> mesh_type [[stick_ball_ratio]] <br /> mesh_width stick_color <br /> min_mesh_spacing stick_fixed_radius <br /> mouse_limit [[stick_nub]] <br /> mouse_restart_movie_delay stick_overlap <br /> mouse_scale stick_quality <br /> mouse_selection_mode stick_radius <br /> movie_delay [[stick_transparency]] <br /> movie_loop stick_valence_scale <br /> multiplex stop_on_exceptions <br /> no_idle surface_best <br /> nonbonded_size surface_carve_cutoff <br /> normal_workaround surface_carve_selection <br /> normalize_ccp4_maps surface_carve_state <br /> normalize_grd_maps surface_circumscribe <br /> normalize_o_maps surface_clear_cutoff <br /> nvidia_bugs surface_clear_selection <br /> opaque_background surface_clear_state <br /> [[orthoscopic]] surface_color <br /> overlay surface_debug <br /> overlay_lines surface_miserable <br /> pdb_conect_all surface_mode <br /> pdb_discrete_chains surface_normal <br /> pdb_echo_tags surface_optimize_subsets <br /> pdb_hetatm_sort surface_poor <br /> pdb_honor_model_number surface_proximity <br /> pdb_insertions_go_first surface_quality <br /> pdb_insure_orthogonal surface_ramp_above_mode <br /> pdb_literal_names surface_solvent <br /> pdb_no_end_record surface_trim_cutoff <br /> pdb_reformat_names_mode surface_trim_factor <br /> pdb_retain_ids surface_type <br /> pdb_standard_order suspend_updates <br /> pdb_truncate_residue_name swap_dsn6_bytes <br /> pdb_unbond_cations sweep_angle <br /> pdb_use_ter_records sweep_mode <br /> [[pickable]] sweep_phase <br /> png_file_gamma sweep_speed <br /> png_screen_gamma test1 <br /> power test2 <br /> pqr_no_chain_id text <br /> presentation texture_fonts <br /> presentation_auto_quit [[transparency]] <br /> presentation_auto_start transparency_mode <br /> presentation_mode transparency_picking_mode <br /> preserve_chempy_ids triangle_max_passes <br /> pymol_space_max_blue trim_dots <br /> pymol_space_max_green [[two_sided_lighting]]<br /> pymol_space_max_red use_display_lists <br /> pymol_space_min_factor [[valence]] <br /> raise_exceptions valence_default <br /> rank_assisted_sorts valence_size <br /> ray_blend_blue validate_object_names <br /> ray_blend_colors virtual_trackball <br /> ray_blend_green wildcard <br /> ray_blend_red wizard_prompt_mode <br /> ray_color_ramps wrap_output <br /> <br /> [[Category:Settings|All Settings]]</div> TheSmell https://wiki.pymol.org/index.php?title=Cartoon_rect_length&diff=976 Cartoon rect length 2006-11-27T16:08:28Z <p>TheSmell: Created new settings page for cartoon_rect_length</p> <hr /> <div>== Overview ==<br /> <br /> set cartoon_rect_length adjusts how broad the cartoon representation of sheets appear<br /> <br /> == Syntax ==<br /> <br /> &lt;source lang=&quot;python&quot;&gt;<br /> set cartoon_rect_length, &lt;number&gt; #default 1.5<br /> &lt;/source&gt;<br /> <br /> == Example ==<br /> &lt;gallery&gt;<br /> Image:cartoon_rect_length_0.5.png|cartoon_rect_length 0.5<br /> Image:cartoon_rect_width_default.png|cartoon_rect_length 1.5 (default)<br /> Image:cartoon_rect_length_2.0.png|cartoon_rect_length 2.0 <br /> &lt;/gallery&gt;</div> TheSmell https://wiki.pymol.org/index.php?title=File:Cartoon_rect_length_0.5.png&diff=1667 File:Cartoon rect length 0.5.png 2006-11-27T16:08:01Z <p>TheSmell: Image for pymol wiki settings illustarting the cartoon_rect_length setting Created using pymol 0.99 and pdb file 1bgp</p> <hr /> <div>Image for pymol wiki settings illustarting the cartoon_rect_length setting Created using pymol 0.99 and pdb file 1bgp</div> TheSmell https://wiki.pymol.org/index.php?title=File:Cartoon_rect_length_2.0.png&diff=1181 File:Cartoon rect length 2.0.png 2006-11-27T16:07:49Z <p>TheSmell: Image for pymol wiki settings illustarting the cartoon_rect_length setting Created using pymol 0.99 and pdb file 1bgp</p> <hr /> <div>Image for pymol wiki settings illustarting the cartoon_rect_length setting Created using pymol 0.99 and pdb file 1bgp</div> TheSmell