Index

_

__eq__() (Place method) (Places method) __hash__ (Place attribute) (Places attribute) __init__() (Bounds method) (MouseEvent method) (MouseMode method) (MouseModes method) (Place method) (Places method)

__iter__() (Places method) __len__() (Places method) __mul__() (Place method) (Places method)

A

accept_multishadow (Drawing attribute) accept_shadow (Drawing attribute) activate_trigger() (TriggerSet method) add() (LRUSetHistory method) (Model method) (Models method) (OrderedSet method) (Tools method) add_atoms() (Objects method) add_bonds() (Objects method) add_column() (ItemTable method) add_dependency() (TriggerSet method) add_drawing() (Drawing method) add_handler() (TriggerSet method) add_log() (Logger method) add_menu_entry() (MainWindow method) add_menu_selector() (MainWindow method) add_mode() (MouseModes method) add_model() (Objects method) add_model_instances() (Objects method) add_option() (CategorizedOptionsPanel method) (CategorizedSettingsPanel method) (OptionsPanel method) (SettingsPanel method) add_option_group() (CategorizedSettingsPanel method) (SettingsPanel method) add_overlay() (View method) add_presets() (PresetsManager method) add_provider() (OpenManager method) (ProviderManager method) (SaveManager method) add_pseudobonds() (Objects method) add_select_submenu() (MainWindow method) add_settings_option() (MainWindow method) add_surface() (Volume method)

add_tab() (CategorizedOptionsPanel method) (CategorizedSettingsPanel method) ADD_TASK (in module chimerax.core.tasks) ADD_TOOL_INSTANCE (in module chimerax.core.tools) add_trigger() (TriggerSet method) alias() (in module chimerax.std_commands.alias) align() (in module chimerax.std_commands.align) align_points() (in module chimerax.geometry.align) all_drawings() (Drawing method) ALL_EDGES_DISPLAY_MASK (Drawing attribute) all_models() (Model method) all_objects() (in module chimerax.core.commands.atomspec) AllObjects (class in chimerax.core.objects) allow_clipping (Drawing attribute) allow_depth_cue (Drawing attribute) alt_down() (MouseEvent method) ambient_texture (Drawing attribute) ambient_texture_transform (Drawing attribute) ancestor_models() (in module chimerax.core.models) any_part_highlighted() (Drawing method) apply_without_translation() (Place method) array (ArrayGridData attribute) array() (Places method) ArrayGridData (class in chimerax.map_data) assign_id() (Models method) atomic (SelectorInfo attribute) AtomSpec (class in chimerax.core.commands.atomspec) atomspec (Model property) AtomSpecArg (class in chimerax.core.commands.atomspec) attenuate (MotionBlur attribute) AUTO_SAVE (Settings attribute) autostart() (Tools method) axes() (Place method) axes_lengths() (Place method) axis_center_angle_shift() (Place method) axis_length() (Place method)

B

background_color (View property) backing_color (RenderingOptions attribute) bind_mouse_mode() (MouseModes method) bind_standard_mouse_modes() (MouseModes method) bind_texture() (Texture method) bindings (MouseModes property) blend_on_gpu (RenderingOptions attribute) block() (TriggerSet method) block_trigger() (TriggerSet method) BooleanOption (class in chimerax.ui.options.options) bootstrap_bundles() (Toolshed method)

Bounds (class in chimerax.geometry.bounds) bounds() (Drawing method) (Objects method) bounds_intercept_copies() (Drawing method) box_corners() (Bounds method) box_geometry() (in module chimerax.surface.shapes) bt_correction (RenderingOptions attribute) bug() (Logger method) bundle_info() (Toolshed method) BundleAPI (class in chimerax.core.toolshed) BundleInfo (class in chimerax.core.toolshed)

C

cache_data() (BundleInfo method) cage() (in module chimerax.cage_builder.cmd) Camera (class in chimerax.graphics.camera) camera (View property) camera() (in module chimerax.std_commands.camera) camera_framing_drawings() (in module chimerax.graphics.camera) can_set_file_icon() (in module chimerax.core.utils) cap_faces (RenderingOptions attribute) casts_shadows (Drawing attribute) categories (ToolInfo attribute) CategorizedOptionsPanel (class in chimerax.ui.options.containers) CategorizedSettingsPanel (class in chimerax.ui.options.containers) cd() (in module chimerax.std_commands.cd) cell_angles (ArrayGridData attribute) (GridData attribute) center() (Bounds method) changeEvent() (MainWindow method) channel (GridData attribute) child_drawings() (Drawing method) child_models() (Model method) ChildToolWindow (class in chimerax.ui.gui) chimerax.core.commands module chimerax.core.commands.atomspec module chimerax.core.commands.runscript module chimerax.core.configfile module chimerax.core.data_events module chimerax.core.fetch module chimerax.core.history module chimerax.core.logger module chimerax.core.models module chimerax.core.objects module chimerax.core.orderedset module chimerax.core.safesave module chimerax.core.scripting module chimerax.core.serialize module chimerax.core.session module chimerax.core.settings module chimerax.core.tasks module chimerax.core.tools module chimerax.core.toolshed module chimerax.core.triggerset module chimerax.core.utils module chimerax.geometry._geometry module chimerax.geometry.bounds module chimerax.geometry.place module chimerax.geometry.vector module chimerax.graphics.camera module chimerax.graphics.drawing module chimerax.graphics.view module chimerax.io.compression module chimerax.io.io module chimerax.map.volume module chimerax.map_series.vseries_command module chimerax.mouse_modes.mousemodes module chimerax.movie.moviecmd module chimerax.open_command module chimerax.pdb.pdb module chimerax.preset_mgr module chimerax.save_command module

chimerax.segment._segment module chimerax.surface.area module chimerax.surface.gridsurf module chimerax.surface.sasa module chimerax.surface.shapes module chimerax.ui module chimerax.ui.cmd module chimerax.ui.font module chimerax.ui.gui module chimerax.ui.htmltool module chimerax.ui.options.containers module chimerax.ui.options.options module chimerax.ui.widgets.htmlview module chimerax.ui.widgets.item_chooser module chimerax.ui.widgets.item_table module chimerax_bin_dir_first_in_path() (in module chimerax.core.utils) chimerax_binary_directory() (in module chimerax.core.utils) chimerax_intercept() (in module chimerax.ui.widgets.htmlview) ChimeraXHtmlView (class in chimerax.ui.widgets.htmlview) cleanup() (ToolWindow method) clear() (FIFOHistory method) (Logger method) (OrderedSet method) clear_highlight() (Drawing method) clear_special_render_modes() (Camera method) clip() (in module chimerax.std_commands.clip) clip_bounds() (in module chimerax.geometry.bounds) clip_plane_points() (View method) close() (in module chimerax.std_commands.close) (Models method) (SaveFile method) closest_cylinder_intercept() (in module chimerax.geometry._geometry) closest_sphere_intercept() (in module chimerax.geometry._geometry) closest_triangle_intercept() (in module chimerax.geometry._geometry) cofr() (in module chimerax.std_commands.cofr) CollatingLog (class in chimerax.core.logger) Collator (class in chimerax.core.logger) color (Drawing property) (VolumeSurface property) color() (in module chimerax.std_commands.color) color_mode (RenderingOptions attribute) color_modes (RenderingOptions attribute) colormap (Drawing attribute) colormap_extend_left (RenderingOptions attribute) colormap_extend_right (RenderingOptions attribute) colormap_on_gpu (RenderingOptions attribute) colormap_range (Drawing attribute) colormap_size (RenderingOptions attribute) ColorOption (class in chimerax.ui.options.options) colors (Drawing property) (VolumeSurface property) columnCount() (QCxTableModel method) combine_rendered_camera_views() (Camera method) (SplitStereoCamera method) (StereoCamera method) CommandInfo (class in chimerax.core.toolshed) commands (BundleInfo attribute) concatenate_geometry() (in module chimerax.graphics.drawing) cone_geometry() (in module chimerax.surface.shapes) ConfigFile (class in chimerax.core.configfile) confirm_close() (ToolWindow method) coordset() (in module chimerax.std_commands.coordset) copies_bounding_box() (in module chimerax.geometry.bounds) copy_tree_bounds() (in module chimerax.geometry.bounds) cpp_del_model() (Model method) create_child_window() (MainToolWindow method) create_chimerax_profile() (in module chimerax.ui.widgets.htmlview) create_profile() (in module chimerax.ui.widgets.htmlview) cross_product() (in module chimerax.geometry.vector) cross_product_matrix() (in module chimerax.geometry.place) CrossFade (class in chimerax.graphics.crossfade) crossfade() (in module chimerax.std_commands.crossfade) crosslinks() (in module chimerax.crosslinks.crosslinks) crosslinks_histogram() (in module chimerax.crosslinks.crosslinks) crosslinks_minimize() (in module chimerax.crosslinks.crosslinks) crosslinks_network() (in module chimerax.crosslinks.crosslinks) crosssection_midpoints() (in module chimerax.segment._segment) ctrl_down() (MouseEvent method) custom_init (BundleInfo attribute) custom_x3d() (Drawing method) CustomSortString (class in chimerax.core.utils) cylinder_geometry() (in module chimerax.surface.shapes)

D

dashed_cylinder_geometry() (in module chimerax.surface.shapes) data (Volume attribute) data() (QCxTableModel method) data_dir() (BundleAPI static method) (BundleInfo method) decay_factor (MotionBlur attribute) default_color (GridData attribute) DefineSelectorDialog (class in chimerax.ui.gui) delete() (Drawing method) (HtmlToolInstance method) (in module chimerax.std_commands.delete) (Model method) (MotionBlur method) (ToolInstance method) delete_profile() (in module chimerax.ui.widgets.htmlview) delete_texture() (Texture method) delete_trigger() (TriggerSet method) deleted (Model property) deleteLater() (HtmlView method) dependents() (BundleInfo method) dequeue() (FIFOHistory method) deregister() (BundleInfo method) deregister_for_keystrokes() (UI method) deregister_selector() (in module chimerax.core.commands.atomspec) description() (Pick method) (PickedInstance method) (PickedModel method) (PickedTriangle method) (PickedTriangles method) (Place method) destroy() (ItemListWidget method) (ItemMenuButton method) (ItemTable method) (ToolWindow method) determinant() (Place method) devel_alias() (in module chimerax.core.commands.devel) devel_build() (in module chimerax.core.commands.devel) devel_clean() (in module chimerax.core.commands.devel)

devel_dump() (in module chimerax.core.commands.devel) devel_install() (in module chimerax.core.commands.devel) devel_unalias() (in module chimerax.core.commands.devel) device_snav() (in module chimerax.spacenavigator.snav) dim_transparency (RenderingOptions attribute) dim_transparent_voxels (RenderingOptions attribute) discard() (OrderedSet method) dismiss_context_menu() (UI method) display (Drawing property) (Model property) (Volume property) display() (ToolInstance method) display_for_items() (NumericOption method) (Option method) display_help() (ToolInstance method) display_name (ToolInstance attribute) display_positions (Drawing property) display_style (Drawing property) displayed() (Objects method) distance() (in module chimerax.geometry.vector) distribution() (BundleInfo method) Dot (Drawing attribute) double_click (MouseMode attribute) draw() (Drawing method) (MotionBlur method) (View method) draw_background() (Camera method) draw_depth() (in module chimerax.graphics.drawing) draw_highlight_outline() (in module chimerax.graphics.drawing) draw_on_top() (in module chimerax.graphics.drawing) draw_opaque() (in module chimerax.graphics.drawing) draw_overlays() (in module chimerax.graphics.drawing) draw_self() (Drawing method) draw_transparent() (in module chimerax.graphics.drawing) draw_xor_rectangle() (in module chimerax.graphics.drawing) Drawing (class in chimerax.graphics.drawing) drawing_bounds() (View method) drawing_lineage (Drawing property)

E

edge_mask (Drawing property) empty_drawing() (Drawing method) enable() (MouseMode method) enable_stereo() (MainWindow method) enabled (Option property) enclosed_volume() (in module chimerax.surface.area) end_providers() (OpenManager method) (ProviderManager method) (SaveManager method) enqueue() (FIFOHistory method) EnumBase (class in chimerax.ui.options.options) EnumOption (class in chimerax.ui.options.options)

environment variable USERNAME, [1] error() (Logger method) evaluate() (AtomSpec method) everything() (in module chimerax.core.commands.atomspec) executable_dir() (BundleAPI static method) (BundleInfo method) execute() (PresetsManager method) exit() (in module chimerax.std_commands.exit) EXPLICIT_SAVE (Settings attribute) extend() (FIFOHistory method) eye_separation_pixels (StereoCamera attribute) eye_separation_scene (StereoCamera attribute)

F

fetch() (FetcherInfo method) fetch_args (FetcherInfo property) fetch_file() (in module chimerax.core.fetch) FetcherInfo (class in chimerax.open_command) field_of_view (MonoCamera attribute) (StereoCamera attribute) field_width (OrthographicCamera attribute) FIFOHistory (class in chimerax.core.history) file_type (GridData attribute) filename (ConfigFile property) FileOption (class in chimerax.ui.options.options) fill_context_menu() (ToolWindow method) find_bundle() (Toolshed method) find_bundle_for_class() (Toolshed method) find_bundle_for_command() (Toolshed method) find_bundle_for_tool() (Toolshed method) find_by_class() (Tasks method) (Tools method) find_close_points() (in module chimerax.geometry._geometry) find_close_points_sets() (in module chimerax.geometry._geometry)

find_closest_points() (in module chimerax.geometry._geometry) find_local_maxima() (in module chimerax.segment._segment) finish() (BundleAPI static method) (BundleInfo method) finish_rendering() (View method) first_intercept() (Drawing method) (Model method) first_intercept_children() (Drawing method) fitmap() (in module chimerax.map_fit.fitcmd) flags() (QCxTableModel method) flattened() (in module chimerax.core.utils) flip_normals (RenderingOptions attribute) FloatEnumOption (class in chimerax.ui.options.options) FloatOption (class in chimerax.ui.options.options) FontOption (class in chimerax.ui.options.options) forward_keystroke() (UI method) frame_buffer_rgba() (View method) from_cache_data() (BundleInfo class method) frustum() (in module chimerax.graphics.camera) full_region_on_gpu (RenderingOptions attribute)

G

geometry_bounds() (Drawing method) get_attribute() (Option method) get_class() (BundleAPI static method) (BundleInfo method) get_module() (BundleInfo method) get_selected() (Model method)

get_selector() (in module chimerax.core.commands.atomspec) get_selector_description() (in module chimerax.core.commands.atomspec) get_toolshed() (in module chimerax.core.toolshed) graphics() (in module chimerax.std_commands.graphics) grid_id (GridData attribute) GridData (class in chimerax.map_data)

H

has_formatted_metadata() (Model method) has_handlers() (TriggerSet method) has_trigger() (TriggerSet method) headerData() (QCxTableModel method) help (ToolInstance attribute) help() (in module chimerax.help_viewer.cmd) hidden_args (SaverInfo property) hide() (in module chimerax.std_commands.hide) highlight_color (View property) HIGHLIGHT_DRAW_PASS (Drawing attribute) highlight_thickness (View property)

highlighted (Drawing property) highlighted_displayed_triangles_mask (Drawing property) highlighted_positions (Drawing property) highlighted_triangles_mask (Drawing property) HostPortOption (class in chimerax.ui.options.options) html_name() (Annotation method) html_to_plain() (in module chimerax.core.logger) html_user_agent() (in module chimerax.core.fetch) HtmlLog (class in chimerax.core.logger) HtmlToolInstance (class in chimerax.ui.htmltool) HtmlView (class in chimerax.ui.widgets.htmlview)

I

icon_file (MouseMode attribute) id (Model attribute) (Task attribute) id_string (Model property) (PickedTriangle property) identity() (in module chimerax.geometry.place) ijk_to_xyz() (GridData method) image() (View method) image_mode (RenderingOptions attribute) image_rgba() (View method) import_bundle() (Toolshed method) in_file_history (FetcherInfo property) (OpenerInfo property) (SaverInfo property) include_dir() (BundleAPI static method) (BundleInfo method) info() (Logger method) inherit_graphics_exemptions (Drawing attribute) init() (in module chimerax.core.toolshed) init_manager() (BundleAPI static method) (BundleInfo method) initial_camera_view() (View method) initialize() (BundleAPI static method) (BundleInfo method) initialize_ssl_cert_dir() (in module chimerax.core.utils)

InitWindowSizeOption (class in chimerax.ui.gui) inner_product() (in module chimerax.geometry.vector) inner_product_64() (in module chimerax.geometry._geometry) InputFileOption (class in chimerax.ui.options.options) InputFolderOption (class in chimerax.ui.options.options) install_bundle() (Toolshed method) installed (BundleInfo attribute) interface_values() (in module chimerax.segment._segment) interfaces() (in module chimerax.interfaces.cmd) interpolate() (Place method) interpolate_rotation() (in module chimerax.geometry.place) interpolate_scene() (Model method) IntOption (class in chimerax.ui.options.options) inverse() (Place method) is_blocked() (TriggerSet method) is_identity() (Place method) (Places method) is_selector_atomic() (in module chimerax.core.commands.atomspec) is_selector_user_defined() (in module chimerax.core.commands.atomspec) is_trigger_blocked() (TriggerSet method) issubset() (OrderedSet method) issuperset() (OrderedSet method) ItemListWidget (class in chimerax.ui.widgets.item_chooser) ItemMenuButton (class in chimerax.ui.widgets.item_chooser) ItemTable (class in chimerax.ui.widgets.item_table)

J

Job (class in chimerax.core.tasks) JobError

JobLaunchError JobMonitorError

K

ks() (in module chimerax.shortcuts.shortcuts)

L

label() (in module chimerax.label.label3d) label_change() (in module chimerax.label.label2d) label_create() (in module chimerax.label.label2d) label_delete() (in module chimerax.label.label2d) (in module chimerax.label.label3d) LabelHeightDialog (class in chimerax.ui.gui) LAST_DRAW_PASS (Drawing attribute) last_mouse_position (MouseMode attribute) lessThan() (NumSortingProxyModel method) level (VolumeSurface property) LEVEL_BUG (Log attribute) LEVEL_ERROR (Log attribute) LEVEL_INFO (Log attribute) LEVEL_WARNING (Log attribute) library_dir() (BundleAPI static method) (BundleInfo method) Lighting (class in chimerax.graphics.opengl) lighting (View property) lighting() (in module chimerax.std_commands.lighting) limit_voxel_count (RenderingOptions attribute)

line_thickness (RenderingOptions attribute) linear_interpolation (RenderingOptions attribute) list() (Tasks method) (Tools method) list_selectors() (in module chimerax.core.commands.atomspec) load() (ObjectHistory method) Log (class in chimerax.core.logger) log() (CollatingLog method) (HtmlLog method) (in module chimerax.log.cmd) (Log method) (MainWindow method) (PlainTextLog method) (StringPlainTextLog method) log_version() (in module chimerax.core.logger) Logger (class in chimerax.core.logger) logger (Session attribute) look_at() (in module chimerax.geometry.place) lower() (CustomSortString method) LRUSetHistory (class in chimerax.core.history)

M

main_view (MainWindow property) (Session attribute) MainToolWindow (class in chimerax.ui.gui) MainWindow (class in chimerax.ui.gui) make_callback() (Option method) make_link() (in module chimerax.core.utils) manage() (ToolWindow method) manual_block() (TriggerSet method) manual_release() (TriggerSet method) mask() (in module chimerax.mask.maskcommand) masked() (Places method) Material (class in chimerax.graphics.opengl) material (View property) material() (in module chimerax.std_commands.material) matrix (Place property) matrix() (GridData method) maximum_intensity_projection (RenderingOptions attribute) measure_buriedarea() (in module chimerax.std_commands.measure_buriedarea) measure_convexity() (in module chimerax.std_commands.measure_convexity) measure_length() (in module chimerax.std_commands.measure_length) MenuButton (class in chimerax.ui.widgets.item_chooser) Mesh (Drawing attribute) mesh_lighting (RenderingOptions attribute) metadata (Session attribute) migrate_from() (ConfigFile method) migrate_value() (ConfigFile method) minimal_texture_memory (RenderingOptions attribute) mlp() (in module chimerax.mlp.mlp) mod_key_info() (in module chimerax.mouse_modes.mousemodes) (ItemListWidget method) mode() (MouseModes method) Model (class in chimerax.core.models) ModelListWidget (class in chimerax.ui.widgets.item_chooser) ModelMenuButton (class in chimerax.ui.widgets.item_chooser) Models (class in chimerax.core.models) models (Session attribute) modes (MouseModes property) module chimerax.core.commands chimerax.core.commands.atomspec chimerax.core.commands.runscript chimerax.core.configfile chimerax.core.data_events chimerax.core.fetch chimerax.core.history chimerax.core.logger chimerax.core.models chimerax.core.objects chimerax.core.orderedset chimerax.core.safesave chimerax.core.scripting chimerax.core.serialize chimerax.core.session chimerax.core.settings chimerax.core.tasks chimerax.core.tools chimerax.core.toolshed chimerax.core.triggerset chimerax.core.utils chimerax.geometry._geometry chimerax.geometry.bounds chimerax.geometry.place chimerax.geometry.vector chimerax.graphics.camera chimerax.graphics.drawing chimerax.graphics.view chimerax.io.compression chimerax.io.io chimerax.map.volume chimerax.map_series.vseries_command chimerax.mouse_modes.mousemodes chimerax.movie.moviecmd chimerax.open_command chimerax.pdb.pdb chimerax.preset_mgr chimerax.save_command chimerax.segment._segment chimerax.surface.area chimerax.surface.gridsurf chimerax.surface.sasa chimerax.surface.shapes chimerax.ui chimerax.ui.cmd chimerax.ui.font chimerax.ui.gui chimerax.ui.htmltool chimerax.ui.options.containers chimerax.ui.options.options chimerax.ui.widgets.htmlview chimerax.ui.widgets.item_chooser chimerax.ui.widgets.item_table

molmap() (in module chimerax.map.molmap) monitor() (Job method) MonoCamera (class in chimerax.graphics.camera) morph() (in module chimerax.morph.morph) MotionBlur (class in chimerax.graphics.crossfade) mouse_double_click() (MouseMode method) mouse_down() (MouseMode method) mouse_down_position (MouseMode attribute) mouse_drag() (MouseMode method) mouse_motion() (MouseMode method) mouse_pause_tracking() (MouseModes method) mouse_up() (MouseMode method) MouseEvent (class in chimerax.mouse_modes.mousemodes) MouseMode (class in chimerax.mouse_modes.mousemodes) mousemode() (in module chimerax.mouse_modes.cmd) MouseModes (class in chimerax.mouse_modes.mousemodes) move() (in module chimerax.std_commands.move) (View method) move_after_pause() (MouseMode method) movie_abort() (in module chimerax.movie.moviecmd) movie_crossfade() (in module chimerax.movie.moviecmd) movie_duplicate() (in module chimerax.movie.moviecmd) movie_encode() (in module chimerax.movie.moviecmd) movie_formats() (in module chimerax.movie.moviecmd) movie_ignore() (in module chimerax.movie.moviecmd) movie_record() (in module chimerax.movie.moviecmd) movie_reset() (in module chimerax.movie.moviecmd) movie_status() (in module chimerax.movie.moviecmd) movie_stop() (in module chimerax.movie.moviecmd) mseries() (in module chimerax.model_series.mseries) mseries_slider() (in module chimerax.model_series.mseries) multiply_transforms() (in module chimerax.geometry.place) multitexture (Drawing attribute) multitexture_reverse_order (Drawing attribute)

N

name (Annotation attribute) (ArrayGridData attribute) (BundleInfo property) (Camera attribute) (Drawing attribute) (GridData attribute) (Model property) (MonoCamera attribute) (MouseMode attribute) (OrthographicCamera attribute) (SaveFile attribute) (SelectorInfo attribute) (SplitStereoCamera attribute) (StereoCamera attribute) (ToolInfo attribute) (Volume property) natural_cubic_spline() (in module chimerax.geometry._geometry)

near_far_distances() (View method) new_drawing() (Drawing method) new_region() (Volume method) newer_than() (BundleInfo method) NewerVersionQuery (class in chimerax.core.toolshed) norm() (in module chimerax.geometry.vector) normalization() (Texture method) normalize_vector() (in module chimerax.geometry.vector) normalize_vectors() (in module chimerax.geometry.vector) normals (Drawing property) number_of_positions() (Drawing method) number_of_triangles() (Drawing method) number_of_views() (Camera method) (SplitStereoCamera method) (StereoCamera method) NumericOption (class in chimerax.ui.options.options) NumSortingProxyModel (class in chimerax.ui.widgets.item_table)

O

ObjectHistory (class in chimerax.core.history) Objects (class in chimerax.core.objects) octahedron_geometry() (in module chimerax.surface.shapes) on_disk() (ConfigFile method) on_finish() (NewerVersionQuery method) (Task method) on_top (Drawing attribute) ones_mask() (in module chimerax.mask.maskcommand) OPAQUE_DRAW_PASS (Drawing attribute) opaque_texture (Drawing attribute) open() (OpenerInfo method) open_args (OpenerInfo property) open_command_script() (in module chimerax.core.scripting) open_compiled_python_script() (in module chimerax.core.scripting) open_data() (OpenManager method) open_data_formats (OpenManager property) open_input() (in module chimerax.io.io) open_map() (in module chimerax.map.volume) open_output() (in module chimerax.io.io) open_pdb() (in module chimerax.pdb.pdb) open_python_script() (in module chimerax.core.scripting) OpenerInfo (class in chimerax.open_command) opengl_matrices() (Places method)

opengl_matrix() (Place method) OpenManager (class in chimerax.open_command.manager) Option (class in chimerax.ui.options.options) OptionalRGBA8PairOption (class in chimerax.ui.options.options) OptionalRGBAOption (class in chimerax.ui.options.options) OptionalRGBAPairOption (class in chimerax.ui.options.options) OptionsPanel (class in chimerax.ui.options.containers) OrderedSet (class in chimerax.core.orderedset) OrderedWeakrefSet (class in chimerax.core.orderedset) origin (ArrayGridData attribute) (GridData attribute) origin() (Place method) ortho() (in module chimerax.graphics.camera) OrthographicCamera (class in chimerax.graphics.camera) orthonormal_frame() (in module chimerax.geometry.place) orthoplane_positions (RenderingOptions attribute) orthoplanes_shown (RenderingOptions attribute) outline_box_rgb (RenderingOptions attribute) OutputFileOption (class in chimerax.ui.options.options) OutputFolderOption (in module chimerax.ui.options.options) overall_color (Model property) (Volume property) (VolumeImage property) overlays() (View method)

P

parse() (AtomSpecArg class method) (SeriesArg class method) PasswordOption (class in chimerax.ui.options.options) path (GridData attribute) pause() (MouseMode method) perframe() (in module chimerax.std_commands.perframe) perspective_direction() (in module chimerax.graphics.camera) perspective_projection_matrix() (in module chimerax.graphics.camera) perspective_view_all() (in module chimerax.graphics.camera) perspective_view_width() (in module chimerax.graphics.camera) PhysicalSizeOption (class in chimerax.ui.options.options) Pick (class in chimerax.graphics.drawing) pickable (Drawing attribute) picked_object() (View method) picked_object_on_segment() (View method) PickedInstance (class in chimerax.graphics.drawing) PickedModel (class in chimerax.core.models) PickedTriangle (class in chimerax.graphics.drawing) PickedTriangles (class in chimerax.graphics.drawing) pickle_deserialize() (in module chimerax.core.serialize) pixel_size() (MouseMode method) (View method) Place (class in chimerax.geometry.place) place_list() (Places method) placements (ToolWindow attribute)

Places (class in chimerax.geometry.place) PlainTextLog (class in chimerax.core.logger) plane_spacing (RenderingOptions attribute) planes_pick() (Drawing method) point_bounds() (in module chimerax.geometry.bounds) position (Camera property) (Drawing property) (Model property) position() (MouseEvent method) position_rgba_drawing() (in module chimerax.graphics.drawing) positions (Drawing property) (Model property) PresetsManager (class in chimerax.preset_mgr.manager) product() (in module chimerax.geometry.place) profile (HtmlView attribute) profile_trigger() (TriggerSet method) projection_matrix() (Camera method) (OrthographicCamera method) projection_mode (RenderingOptions attribute) projection_modes (RenderingOptions attribute) PROPERTY_INFO (ConfigFile attribute) ProviderManager (class in chimerax.core.toolshed) pwd() (in module chimerax.std_commands.pwd) Python Enhancement Proposals PEP 484 PEP 8

Q

QCxTableModel (class in chimerax.ui.widgets.item_table)

quaternion_rotation() (in module chimerax.geometry.place)

R

radius() (Bounds method) rainbow() (in module chimerax.std_commands.rainbow) ray() (Camera method) (MonoCamera method) (OrthographicCamera method) (SplitStereoCamera method) (StereoCamera method) ray_step (RenderingOptions attribute) read_matrix() (GridData method) read_texture_data() (Texture method) rectangle_bounding_planes() (Camera method) rectangle_pick() (View method) redraw_needed (Camera attribute) redraw_needed() (Drawing method) region (Volume attribute) region_bounds() (in module chimerax.segment._segment) region_contacts() (in module chimerax.segment._segment) region_index_lists() (in module chimerax.segment._segment) region_maxima() (in module chimerax.segment._segment) region_point_count() (in module chimerax.segment._segment) region_points() (in module chimerax.segment._segment) register() (BundleInfo method) register_command() (BundleAPI static method) register_for_keystrokes() (UI method) register_selector() (BundleAPI static method) (in module chimerax.core.commands.atomspec) register_snapshot_methods() (Session method) release() (TriggerSet method) reload() (Toolshed method) reload_texture() (Texture method) remove() (Models method) (Tools method) remove_all_drawings() (Drawing method) remove_binding() (MouseModes method) remove_drawing() (Drawing method) remove_drawings() (Drawing method) remove_handler() (TriggerSet method) remove_log() (Logger method) remove_mode() (MouseModes method) remove_overlays() (View method) remove_scale() (Place method) remove_surfaces() (Volume method) REMOVE_TASK (in module chimerax.core.tasks) REMOVE_TOOL_INSTANCE (in module chimerax.core.tools) rename() (in module chimerax.std_commands.rename) rendering_options (Volume attribute) RenderingOptions (class in chimerax.map.volume) replace() (FIFOHistory method)

report_exception() (Logger method) report_framerate() (View method) reset() (ConfigFile method) (Session method) (Settings method) reset_state() (Models method) (Tasks method) (Tools method) (UserAliases method) resfit() (in module chimerax.residue_fit.cmd) resize() (View method) restore() (Session method) (Settings method) (Task method) restore_geometry() (Model method) restore_scene() (Model method) restore_snapshot() (Model class method) (Models static method) (NewerVersionQuery class method) (Surface class method) (Task class method) (Tasks static method) (ToolInstance class method) (Tools static method) (UserAliases class method) retrieve_url() (in module chimerax.core.fetch) rgba (VolumeSurface property) RGBA8Option (class in chimerax.ui.options.options) rgba_drawing() (in module chimerax.graphics.drawing) RGBAOption (class in chimerax.ui.options.options) roll() (in module chimerax.std_commands.roll) rotate() (View method) rotation (ArrayGridData attribute) (GridData attribute) rotation() (in module chimerax.geometry.place) rotation_angle() (Place method) rotation_axis_and_angle() (Place method) rotation_quaternion() (Place method) round_off() (in module chimerax.core.utils) rowCount() (QCxTableModel method) run() (in module chimerax.core.commands) (Job method) (NewerVersionQuery method) (Task method) run_provider() (BundleAPI static method) (BundleInfo method) runJavaScript() (HtmlView method) running() (Job method) runscript() (in module chimerax.core.commands.runscript)

S

same() (Place method) save() (ConfigFile method) (FIFOHistory method) (in module chimerax.core.session) (LRUSetHistory method) (ObjectHistory method) (SaverInfo method) (Session method) (Settings method) save_args (SaverInfo property) save_args_string_from_widget() (SaverInfo method) save_args_widget() (SaverInfo method) save_data() (SaveManager method) save_data_formats (SaveManager property) save_geometry() (Model method) save_map() (in module chimerax.map.volume) save_pdb() (in module chimerax.pdb.pdb) SaveBinaryFile (class in chimerax.core.safesave) SaveFile (class in chimerax.core.safesave) SaveManager (class in chimerax.save_command.manager) SaverInfo (class in chimerax.save_command) SaveTextFile (class in chimerax.core.safesave) scale() (in module chimerax.geometry.place) scale_factor() (Place method) scale_translation() (Place method) scene_position (Drawing property) scroll_to() (ItemTable method) sdump() (in module chimerax.core.session) segmentation_surface() (in module chimerax.segment._segment) segmentation_surfaces() (in module chimerax.segment._segment) SelContactsDialog (class in chimerax.ui.gui) select() (in module chimerax.std_commands.select) (Pick method) (PickedInstance method) (PickedModel method) (PickedTriangle method) (PickedTriangles method) select_by_mode() (MainWindow method) selected (Model property) SelectorInfo (class in chimerax.core.toolshed) SelSeqDialog (class in chimerax.ui.gui) SelZoneDialog (class in chimerax.ui.gui) SeriesArg (class in chimerax.map_series.vseries_command) ses_surface_geometry() (in module chimerax.surface.gridsurf) Session (class in chimerax.core.session) session (Task property) (Tasks property) (ToolInstance property) (Volume attribute) SESSION_ENDURING (Model attribute) (Task attribute) (ToolInstance attribute) SESSION_SAVE (Model attribute) (Task attribute) (ToolInstance attribute) SESSION_SUFFIX (in module chimerax.core.session) session_versions (BundleInfo attribute) SESSION_WARN (Model attribute) session_write_version (BundleInfo attribute) set() (in module chimerax.std_commands.set) set_attribute() (Option method) set_bonds() (Objects method) set_brightness() (VolumeSurface method) set_default_parameters() (Lighting method) (Material method) set_display_style() (Volume method) set_fatal_error_log_file() (UI method) set_file_icon() (in module chimerax.core.utils) set_fixed_pixel_shift() (Camera method) set_geometry() (Drawing method) set_linear_interpolation() (Texture method) set_multiple() (BooleanOption method) (EnumBase method) (FileOption method) (FloatEnumOption method) (FloatOption method) (InitWindowSizeOption method) (InputFolderOption method) (IntOption method) (Option method) (OptionalRGBA8PairOption method) (RGBA8Option method) (StringIntOption method) (StringOption method) (StringsOption method) set_parameters() (Volume method) set_pseudobonds() (Objects method) set_render_target() (Camera method) (SplitStereoCamera method) (StereoCamera method) set_rotation_depth() (View method)

set_special_render_modes() (Camera method) set_transparency() (Drawing method) (Volume method) (VolumeSurface method) set_user_agent() (in module chimerax.ui.widgets.htmlview) set_value() (OptionalRGBA8PairOption method) (RGBA8Option method) setData() (QCxTableModel method) setHtml() (HtmlView method) Settings (class in chimerax.core.settings) SettingsPanel (class in chimerax.ui.options.containers) SettingsPanelBase (class in chimerax.ui.options.containers) setUrl() (HtmlView method) shape_changed (Drawing property) shift_and_angle() (Place method) shift_and_scale_array() (Places method) shift_down() (MouseEvent method) short_name (BundleInfo property) show() (in module chimerax.std_commands.show) (Volume method) show_metadata() (Model method) show_outline_box (RenderingOptions attribute) show_outline_box() (Volume method) show_text() (FloatOption method) (IntOption method) (NumericOption method) showing_transparent() (Drawing method) shown (ToolWindow property) shown_changed() (ToolWindow method) shrink_to_fit() (ToolWindow method) silhouette (View property) size (GridData attribute) size() (Bounds method) (in module chimerax.std_commands.size) sizeHint() (HtmlView method) sizeHintForColumn() (ItemTable method) skew_axes() (in module chimerax.geometry.place) skip_bounds (Drawing attribute) smooth_lines (RenderingOptions attribute) smoothing_factor (RenderingOptions attribute) smoothing_iterations (RenderingOptions attribute) smoothlines() (in module chimerax.smooth_lines.smoothlines) snapshot_methods() (Session method) Solid (Drawing attribute) specifier() (Pick method) (PickedModel method) sphere_bounds() (in module chimerax.geometry.bounds) sphere_geometry() (in module chimerax.surface.shapes) sphere_geometry2() (in module chimerax.surface.shapes) spheres_surface_area() (in module chimerax.surface.sasa) split() (in module chimerax.std_commands.split) SplitStereoCamera (class in chimerax.graphics.camera) square_mesh (RenderingOptions attribute) standard_metadata() (in module chimerax.core.session) start() (Task method) start_tool() (BundleAPI static method) (BundleInfo method) start_tools() (Tools method) state (Task attribute) status() (Log method) (Logger method) (MainWindow method) (StatusLogger method) (ToolWindow method) StatusLogger (class in chimerax.core.logger) step (ArrayGridData attribute) (GridData attribute) stereo_scaling() (View method) StereoCamera (class in chimerax.graphics.camera) stop() (in module chimerax.std_commands.stop) StringIntOption (class in chimerax.ui.options.options) StringOption (class in chimerax.ui.options.options) StringPlainTextLog (class in chimerax.core.logger) StringsOption (class in chimerax.ui.options.options) struts() (in module chimerax.struts.struts) struts_delete() (in module chimerax.struts.struts) style() (in module chimerax.std_commands.style) subdivide_surface (RenderingOptions attribute) subdivision_levels (RenderingOptions attribute) Surface (class in chimerax.core.models) surface_area() (in module chimerax.surface.area) surface_bounds() (Volume method) surface_smoothing (RenderingOptions attribute) surface_volume_and_area() (in module chimerax.surface.area) surfaces (Volume property) sym() (in module chimerax.std_commands.sym) SymbolicEnumOption (class in chimerax.ui.options.options) symmetries (ArrayGridData attribute) (GridData attribute) synopsis (BundleInfo property) (SelectorInfo attribute) (ToolInfo attribute)

T

take_snapshot() (Model method) (Models method) (NewerVersionQuery method) (Task method) (Tasks method) (ToolInstance method) (Tools method) (UserAliases method) Task (class in chimerax.core.tasks) Tasks (class in chimerax.core.tasks) TaskState (class in chimerax.core.tasks) terminate() (Task method) terminated() (Task method) terminating() (Task method) tetrahedron_geometry() (in module chimerax.surface.shapes) text_image_rgba() (in module chimerax.graphics.drawing) Texture (class in chimerax.graphics.opengl) texture (Drawing attribute) texture_coordinates (Drawing attribute) texture_format() (Texture method) thread_safe() (UI method) tilted_slab_axis (RenderingOptions attribute) tilted_slab_offset (RenderingOptions attribute) tilted_slab_plane_count (RenderingOptions attribute) tilted_slab_spacing (RenderingOptions attribute) time (GridData attribute) time() (in module chimerax.std_commands.time) title (ToolWindow property) ToolInfo (class in chimerax.core.toolshed) ToolInstance (class in chimerax.core.tools) tools (BundleInfo attribute) Tools (class in chimerax.core.tools) Toolshed (class in chimerax.core.toolshed) TOOLSHED_BUNDLE_INFO_ADDED (in module chimerax.core.toolshed) TOOLSHED_BUNDLE_INFO_RELOADED (in module chimerax.core.toolshed) TOOLSHED_BUNDLE_INSTALLED (in module chimerax.core.toolshed) TOOLSHED_BUNDLE_UNINSTALLED (in module chimerax.core.toolshed) toolshed_install() (in module chimerax.core.commands.toolshed) toolshed_list() (in module chimerax.core.commands.toolshed)

TOOLSHED_OUT_OF_DATE_BUNDLES (in module chimerax.core.toolshed) toolshed_reload() (in module chimerax.core.commands.toolshed) toolshed_uninstall() (in module chimerax.core.commands.toolshed) toolshed_url() (in module chimerax.core.commands.toolshed) ToolshedError ToolshedInitializationError ToolshedInstalledError ToolshedUnavailableError ToolSideOption (class in chimerax.ui.gui) ToolWindow (class in chimerax.ui.gui) touchpad_four_finger_trans() (MouseMode method) touchpad_three_finger_trans() (MouseMode method) touchpad_two_finger_scale() (MouseMode method) touchpad_two_finger_trans() (MouseMode method) touchpad_two_finger_twist() (MouseMode method) trackpad_mode() (MouseModes method) transform_coordinates() (Places method) transform_normals() (Place method) transform_planes() (in module chimerax.geometry.place) transform_points() (Place method) transform_vector() (Place method) transform_vectors() (Place method) translate() (View method) translation() (in module chimerax.geometry.place) (Place method) transparency() (in module chimerax.std_commands.transparency) TRANSPARENT_DEPTH_DRAW_PASS (Drawing attribute) TRANSPARENT_DRAW_PASS (Drawing attribute) transpose() (Place method) triangle_mask (Drawing property) triangles (Drawing property) trigger_handlers() (TriggerSet method) trigger_names() (TriggerSet method) triggers (Session attribute) (Settings attribute) (Toolshed attribute) TriggerSet (class in chimerax.core.triggerset) turn() (in module chimerax.std_commands.turn) two_sided_lighting (RenderingOptions attribute)

U

UI (class in chimerax.ui.gui) ui_autostart() (in module chimerax.ui.cmd) ui_dockable() (in module chimerax.ui.cmd) ui_favorite() (in module chimerax.ui.cmd) ui_fullscreen() (in module chimerax.ui.cmd) ui_hide_floating() (in module chimerax.ui.cmd) ui_menubar() (in module chimerax.ui.cmd) ui_statusbar() (in module chimerax.ui.cmd) ui_tool_hide() (in module chimerax.ui.cmd) ui_tool_show() (in module chimerax.ui.cmd) ui_windowfill() (in module chimerax.ui.cmd) unbind_texture() (Texture method)

uninstall_bundle() (Toolshed method) union() (OrderedSet method) union_bounds() (in module chimerax.geometry.bounds) unload() (BundleInfo method) UnwantedCompressionError update() (ConfigFile method) (Settings method) upper() (CustomSortString method) url (Annotation attribute) use_lighting (Drawing attribute) UserAliases (class in chimerax.core.session) USERNAME, [1] uses_wheel (MouseMode property)

V

value (BooleanOption property) Value (class in chimerax.core.configfile) value (ColorOption property) (EnumBase property) (FileOption property) (FloatEnumOption property) (FloatOption property) (InitWindowSizeOption property) (InputFolderOption property) (IntOption property) (Option property) (OptionalRGBA8PairOption property) (OptionalRGBAOption property) (OptionalRGBAPairOption property) (RGBA8Option property) (RGBAOption property) (StringIntOption property) (StringOption property) (StringsOption property) value_type (GridData attribute) values (FontOption attribute) values_for_items() (Option method) vector_rotation() (in module chimerax.geometry.place) vector_sum() (in module chimerax.geometry.vector) version (BundleInfo property) vertex_colors (Drawing property) vertices (Drawing property) View (class in chimerax.graphics.view) view() (Camera method) (in module chimerax.std_commands.view) (SplitStereoCamera method) (StereoCamera method) view_all() (Camera method) (MonoCamera method) (OrthographicCamera method) (SplitStereoCamera method) (StereoCamera method) (View method) view_delete() (in module chimerax.std_commands.view) view_direction() (Camera method) view_initial() (in module chimerax.std_commands.view) view_list() (in module chimerax.std_commands.view) view_matrix() (in module chimerax.std_commands.view) view_name() (in module chimerax.std_commands.view) view_pixel_shift() (Camera method) (StereoCamera method) view_width() (Camera method) (MonoCamera method) (OrthographicCamera method) (SplitStereoCamera method) (StereoCamera method)

Volume (class in chimerax.map) volume() (in module chimerax.map.volumecommand) volume_add() (in module chimerax.map_filter.vopcommand) volume_bin() (in module chimerax.map_filter.vopcommand) volume_boxes() (in module chimerax.map_filter.vopcommand) volume_copy() (in module chimerax.map_filter.vopcommand) volume_cover() (in module chimerax.map_filter.vopcommand) volume_erase() (in module chimerax.map_eraser.eraser) volume_falloff() (in module chimerax.map_filter.vopcommand) volume_flatten() (in module chimerax.map_filter.vopcommand) volume_flip() (in module chimerax.map_filter.vopcommand) volume_fourier() (in module chimerax.map_filter.vopcommand) volume_from_grid_data() (in module chimerax.map) volume_gaussian() (in module chimerax.map_filter.vopcommand) volume_laplacian() (in module chimerax.map_filter.vopcommand) volume_local_correlation() (in module chimerax.map_filter.vopcommand) volume_maximum() (in module chimerax.map_filter.vopcommand) volume_median() (in module chimerax.map_filter.vopcommand) volume_minimum() (in module chimerax.map_filter.vopcommand) volume_morph() (in module chimerax.map_filter.vopcommand) volume_multiply() (in module chimerax.map_filter.vopcommand) volume_new() (in module chimerax.map_filter.vopcommand) volume_octant() (in module chimerax.map_filter.vopcommand) volume_permute_axes() (in module chimerax.map_filter.vopcommand) volume_resample() (in module chimerax.map_filter.vopcommand) volume_ridges() (in module chimerax.map_filter.vopcommand) volume_scale() (in module chimerax.map_filter.vopcommand) volume_subtract() (in module chimerax.map_filter.vopcommand) volume_threshold() (in module chimerax.map_filter.vopcommand) volume_tile() (in module chimerax.map_filter.vopcommand) volume_unbend() (in module chimerax.map_filter.vopcommand) volume_unroll() (in module chimerax.map_filter.vopcommand) volume_unzone() (in module chimerax.map_filter.vopcommand) volume_zone() (in module chimerax.map_filter.vopcommand) VolumeImage (class in chimerax.map) VolumeSurface (class in chimerax.map) voxel_count() (GridData method) voxel_limit (RenderingOptions attribute) voxel_volume() (GridData method) vr() (in module chimerax.vive.vr) vseries_align() (in module chimerax.map_series.vseries_command) vseries_measure() (in module chimerax.map_series.vseries_command) vseries_play() (in module chimerax.map_series.vseries_command) vseries_save() (in module chimerax.map_series.vseries_command) vseries_slider() (in module chimerax.map_series.vseries_command) vseries_stop() (in module chimerax.map_series.vseries_command)

W

wait() (in module chimerax.std_commands.wait) warning() (Logger method) was_deleted (Drawing attribute) watershed_regions() (in module chimerax.segment._segment) wheel() (MouseMode method) wheel_value() (MouseEvent method)

width() (Bounds method) win_coord() (View method) window_image() (UI method) window_size() (in module chimerax.std_commands.windowsize) writable() (SaveFile method) write() (SaveFile method) writelines() (SaveFile method)

X

xyz_max (Bounds attribute)

xyz_min (Bounds attribute) xyz_to_ijk() (GridData method)

Z

z_align() (in module chimerax.geometry.place) z_axis() (Place method)

zero_translation() (Place method) zoom() (in module chimerax.std_commands.zoom)