Difference between revisions of "Settings"

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Line 34: Line 34:
 
   cache_memory                  ray_transparency_contrast     
 
   cache_memory                  ray_transparency_contrast     
 
   [[cartoon_color]]                  ray_transparency_shadows     
 
   [[cartoon_color]]                  ray_transparency_shadows     
   [[cartoon_cylindrical_helices]]    ray_transparency_spec_cut     
+
   [[Cartoon Helix Settings|cartoon_cylindrical_helices]]    ray_transparency_spec_cut     
 
   cartoon_debug                  ray_transparency_specular     
 
   cartoon_debug                  ray_transparency_specular     
 
   cartoon_discrete_colors        ray_triangle_fudge           
 
   cartoon_discrete_colors        ray_triangle_fudge           
Line 40: Line 40:
 
   cartoon_dumbbell_radius        reflect_power                 
 
   cartoon_dumbbell_radius        reflect_power                 
 
   cartoon_dumbbell_width        retain_order                 
 
   cartoon_dumbbell_width        retain_order                 
   [[cartoon_fancy_helices]]          ribbon_color                 
+
   [[Cartoon Helix Settings|cartoon_fancy_helices]]          ribbon_color                 
 
   [[cartoon_fancy_sheets]]          ribbon_nucleic_acid_mode     
 
   [[cartoon_fancy_sheets]]          ribbon_nucleic_acid_mode     
 
   cartoon_flat_cycles            ribbon_power                 
 
   cartoon_flat_cycles            ribbon_power                 

Revision as of 14:26, 2 June 2006

These are all the PyMol settings. If you feel like documenting them, and what they do, feel free. 6 done, 494 to go !

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