Index

_

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

__iter__() (Collection method) (Places method) __len__() (Collection method) (Places method) __mul__() (Place method) (Places method) __or__() (Collection method) __sub__() (Collection method)

A

accept_multishadow (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) accept_shadow (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) activate_trigger() (TriggerSet method) active_coordset (AtomicStructure property) (Structure property) (StructureData property) active_coordset_change_notify (AtomicStructure property) (Structure property) (StructureData property) active_coordset_id (AtomicStructure property) (Structure property) (StructureData property) active_coordsets (StructureDatas property) add() (AtomicStructure method) (LRUSetHistory method) (Model method) (Models method) (OrderedSet method) (Structure method) (Tools method) add_atom() (CyResidue method) (in module chimerax.atomic.struct_edit) add_atoms() (Objects method) add_bonds() (Objects method) add_citation() (in module chimerax.mmcif.mmcif) add_column() (ItemTable method) add_coordset() (AtomicStructure method) (Structure method) (StructureData method) add_coordsets() (AtomicStructure method) (Structure method) (StructureData method) add_dependency() (TriggerSet method) add_dihedral_atom() (in module chimerax.atomic.struct_edit) add_drawing() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure 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_software() (in module chimerax.mmcif.mmcif) 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_atomic_structures() (in module chimerax.atomic.structure) all_atoms() (in module chimerax.atomic.structure) all_bonds() (in module chimerax.atomic.structure) all_drawings() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) ALL_EDGES_DISPLAY_MASK (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute)

all_models() (AtomicStructure method) (Model method) (Structure method) all_objects() (in module chimerax.core.commands.atomspec) all_pseudobonds() (in module chimerax.atomic.pbgroup) all_residues() (in module chimerax.atomic.structure) all_structures() (in module chimerax.atomic.structure) AllObjects (class in chimerax.core.objects) allow_clipping (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) allow_depth_cue (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) alt_down() (MouseEvent method) alt_loc (CyAtom attribute) alt_loc_change_notifies (StructureDatas property) alt_loc_change_notify (AtomicStructure property) (Structure property) (StructureData property) alt_locs (Atoms property) ambient_texture (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) ambient_texture_transform (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) ancestor_models() (in module chimerax.core.models) aniso_u (Atoms property) (CyAtom attribute) aniso_u6 (Atoms property) (CyAtom attribute) any_part_highlighted() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) append() (Sequence method) apply_without_translation() (Place method) aromatic (Ring property) array (ArrayGridData attribute) array() (Places method) ArrayGridData (class in chimerax.map_data) assembly_html_table() (in module chimerax.atomic.structure) assign_id() (Models method) Atom (class in chimerax.atomic.molobject) atom_count (MolecularSurface property) AtomArg (class in chimerax.atomic.args) atomic (SelectorInfo attribute) AtomicStructure (class in chimerax.atomic.structure) AtomicStructureArg (class in chimerax.atomic.args) AtomicStructureListWidget (class in chimerax.atomic.widgets) AtomicStructureMenuButton (class in chimerax.atomic.widgets) AtomicStructures (class in chimerax.atomic.molarray) AtomicStructuresArg (class in chimerax.atomic.args) atoms (AtomicStructure property) (Bond property) (Bonds property) Atoms (class in chimerax.atomic.molarray) atoms (CyResidue attribute) (Pseudobond property) (Pseudobonds property) (Residues property) (Ring property) (Structure property) (StructureData property) (StructureDatas property) AtomsArg (class in chimerax.atomic.args) AtomsDrawing (class in chimerax.atomic.structure) atomspec (AtomicStructure property) AtomSpec (class in chimerax.core.commands.atomspec) atomspec (Model property) (Structure property) AtomSpecArg (class in chimerax.core.commands.atomspec) attenuate (MotionBlur attribute) AUTO_SAVE (Settings attribute) autochain (AtomicStructure property) (Structure property) autostart() (Tools method) average_ribbon_color (Atoms property) 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) ball_scale (AtomicStructure property) (Structure property) (StructureData property) between_atoms() (Pseudobonds method) bfactor (CyAtom 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) Bond (class in chimerax.atomic.molobject) bond_length() (Element static method) bond_radius() (Element static method) BondArg (class in chimerax.atomic.args) bonded_groups() (AtomicStructure method) (Structure method) (StructureData method) bonds (AtomicStructure property) (Atoms property) Bonds (class in chimerax.atomic.molarray) bonds (CyAtom attribute) (Ring property) (Structure property) (StructureData property) (StructureDatas property) bonds_between() (CyResidue method)

BondsArg (class in chimerax.atomic.args) BondsDrawing (class in chimerax.atomic.structure) BooleanOption (class in chimerax.ui.options.options) bootstrap_bundles() (Toolshed method) Bounds (class in chimerax.geometry.bounds) bounds() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Objects method) (Structure method) bounds_intercept_copies() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) box_corners() (Bounds method) box_geometry() (in module chimerax.surface.shapes) bt_correction (RenderingOptions attribute) bug() (Logger method) bulk_set() (StructureSeq method) bumps() (in module chimerax.bumps.bumps) bundle_info() (Toolshed method) BundleAPI (class in chimerax.core.toolshed) BundleInfo (class in chimerax.core.toolshed) by_chain (Atoms property) (Residues property) by_group (Pseudobonds property) by_structure (Atoms property) (Bonds property) (Residues property)

C

cache_data() (BundleInfo method) cage() (in module chimerax.cage_builder.cmd) calculate_surface_geometry() (MolecularSurface method) 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) cartoon() (in module chimerax.std_commands.cartoon) casts_shadows (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure 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 (CyResidue attribute) center() (Bounds method) centers (Residues property) Chain (class in chimerax.atomic.molobject) chain (CyResidue attribute) chain_id (CyResidue attribute) (StructureSeq property) chain_ids (Chains property) (Residues property) chain_trace_atoms() (AtomicStructure method) (Structure method) (StructureData method) ChainArg (class in chimerax.atomic.args) ChainListWidget (class in chimerax.atomic.widgets) ChainMenuButton (class in chimerax.atomic.widgets) chains (AtomicStructure property) Chains (class in chimerax.atomic.molarray) chains (Residues property) (Structure property) (StructureData property) (StructureDatas property) change_chain_ids() (AtomicStructure method) (Structure method) (StructureData method) change_tracker (AtomicStructure property) (PseudobondGroupData property) (Structure property) (StructureData property) changeEvent() (MainWindow method) ChangeTracker (class in chimerax.atomic.molobject) channel (GridData attribute) characters (Sequence property) (StructureSeq property) child_drawings() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) child_models() (AtomicStructure method) (Model method) (Structure method) ChildToolWindow (class in chimerax.ui.gui) chimerax.atomic.args module chimerax.atomic.cymol module chimerax.atomic.molarray module chimerax.atomic.molobject module chimerax.atomic.molsurf module chimerax.atomic.pbgroup module chimerax.atomic.struct_edit module chimerax.atomic.structure module chimerax.atomic.widgets module 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.list_info.cmd module chimerax.map.volume module chimerax.map_series.vseries_command module chimerax.mmcif.mmcif 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.dust module chimerax.surface.gaussian 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) CIFTable (class in chimerax.mmcif.mmcif) circular (Sequence property) citations() (in module chimerax.mmcif.mmcif) class_obj (in module chimerax.atomic.molobject) clean_alt_locs() (CyResidue method) cleanup() (ToolWindow method) clear() (FIFOHistory method) (Logger method) (OrderedSet method) (PseudobondGroupData method) clear_hide_bits() (Atoms method) (Bond method) (CyAtom method) (Residue method) (Residues method) clear_highlight() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure 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) Collection (class in chimerax.atomic.molarray) color (AtomicStructure property) (AtomsDrawing property) (Bond property) (BondsDrawing property) (CyAtom attribute) (Drawing property) (Pseudobond property) (PseudobondGroupData property) (Structure property) (VolumeSurface property) color() (in module chimerax.std_commands.color) color_atom_patches() (MolecularSurface method) color_cylindrical() (in module chimerax.surface.colorgeom) color_electrostatic() (in module chimerax.surface.colorvol) color_gradient() (in module chimerax.surface.colorvol) color_height() (in module chimerax.surface.colorgeom) color_image() (in module chimerax.surface.texture) color_mode (RenderingOptions attribute) color_modes (RenderingOptions attribute) color_radial() (in module chimerax.surface.colorgeom) color_sample() (in module chimerax.surface.colorvol) color_zone() (in module chimerax.surface.colorzone) colormap (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) colormap_extend_left (RenderingOptions attribute) colormap_extend_right (RenderingOptions attribute) colormap_on_gpu (RenderingOptions attribute) colormap_range (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) colormap_size (RenderingOptions attribute) ColorOption (class in chimerax.ui.options.options) colors (AtomicStructure property) (Atoms property) (AtomsDrawing property) (Bonds property) (BondsDrawing property) (Drawing property) (PseudobondGroupDatas property) (Pseudobonds property) (Structure property) (VolumeSurface property) columnCount() (QCxTableModel method) combine() (AtomicStructure method) (Structure method) combine_rendered_camera_views() (Camera method) (SplitStereoCamera method) (StereoCamera method) combine_sym_atoms() (AtomicStructure method) (Structure method) (StructureData method) CommandInfo (class in chimerax.core.toolshed) commands (BundleInfo attribute) concatenate() (in module chimerax.atomic.molarray) concatenate_geometry() (in module chimerax.graphics.drawing) cone_geometry() (in module chimerax.surface.shapes) ConfigFile (class in chimerax.core.configfile) confirm_close() (ToolWindow method) connect_structure() (AtomicStructure method) (Structure method) (StructureData method) connects_to() (CyAtom method) (CyResidue method) contextmanager() (AtomicStructure method) (Structure method) (StructureData method) coord (CyAtom attribute) coord_index (CyAtom attribute) coord_indices (Atoms property) coords (Atoms property) CoordSet (class in chimerax.atomic.molobject) coordset() (AtomicStructure method) (in module chimerax.std_commands.coordset) (Structure method) (StructureData method) coordset_ids (AtomicStructure property) (Structure property) (StructureData property) coordset_size (AtomicStructure property) (Structure property) (StructureData property) CoordSets (class in chimerax.atomic.molarray) copies_bounding_box() (in module chimerax.geometry.bounds) copy() (AtomicStructure method) (Collection method) (Structure method) copy_tree_bounds() (in module chimerax.geometry.bounds) cpp_del_model() (AtomicStructure method) (Model method) (Structure method) cpp_pointer (AtomicStructure property) (Bond property) (ChangeTracker property) (CoordSet property) (Pseudobond property) (PseudobondGroupData property) (Ring property) (Sequence property) (Structure property) (StructureData property) 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() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) CustomSortString (class in chimerax.core.utils) CyAtom (class in chimerax.atomic.cymol) cylinder_geometry() (in module chimerax.surface.shapes) CyResidue (class in chimerax.atomic.cymol)

D

dashed_cylinder_geometry() (in module chimerax.surface.shapes) dashes (PseudobondGroup property) data (Volume attribute) data() (QCxTableModel method) data_dir() (BundleAPI static method) (BundleInfo method) decay_factor (MotionBlur attribute) default_color (GridData attribute) default_radii (Atoms property) default_radius (CyAtom attribute) DefineSelectorDialog (class in chimerax.ui.gui) delete() (AtomicStructure method) (Atoms method) (AtomsDrawing method) (Bond method) (Bonds method) (BondsDrawing method) (CyAtom method) (CyResidue method) (Drawing method) (HtmlToolInstance method) (in module chimerax.std_commands.delete) (Model method) (MolecularSurface method) (MotionBlur method) (Pseudobond method) (PseudobondGroup method) (Pseudobonds method) (Residues method) (Structure method) (StructureData method) (ToolInstance method) delete_alt_loc() (CyAtom method) (CyResidue method) delete_alt_locs() (AtomicStructure method) (Structure method) (StructureData method) delete_atom() (AtomicStructure method) (Structure method) (StructureData method) delete_bond() (AtomicStructure method) (Structure method) (StructureData method) delete_profile() (in module chimerax.ui.widgets.htmlview) delete_pseudobond() (PseudobondGroupData method) delete_residue() (AtomicStructure method) (Structure method) (StructureData method) delete_texture() (Texture method) delete_trigger() (TriggerSet method) deleted (AtomicStructure property) (Bond property) (ChangeTracker property) (CoordSet property) (CyAtom attribute) (CyResidue attribute) (Model property) (Pseudobond property) (PseudobondGroupData property) (Ring property) (Sequence property) (Structure property) (StructureData 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 (CyResidue attribute) (StructureSeq property) description() (Pick method) (PickedAtom method) (PickedAtoms method) (PickedBond method) (PickedBonds method) (PickedInstance method) (PickedModel method) (PickedPseudobond method) (PickedPseudobonds method) (PickedResidue method) (PickedResidues 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 (AtomicStructure property) (AtomsDrawing property) (Bond property) (BondsDrawing property) (CyAtom attribute) (Drawing property) (Model property) (Pseudobond property) (Structure property) (StructureData property) (Volume property) display() (ToolInstance method) display_for_items() (NumericOption method) (Option method) display_help() (ToolInstance method) display_name (ToolInstance attribute) display_positions (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) display_style (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) displayed() (Objects method) displays (Atoms property) (Bonds property) (Pseudobonds property) distance() (in module chimerax.dist_monitor.cmd) (in module chimerax.geometry.vector) distribution() (BundleInfo method) Dot (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) double_click (MouseMode attribute) draw() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (MotionBlur method) (Structure method) (View method) draw_background() (Camera method) draw_depth() (in module chimerax.graphics.drawing) draw_highlight_outline() (in module chimerax.graphics.drawing) draw_mode (CyAtom attribute) draw_modes (Atoms property) draw_on_top() (in module chimerax.graphics.drawing) draw_opaque() (in module chimerax.graphics.drawing) draw_overlays() (in module chimerax.graphics.drawing) draw_self() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure 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 (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property)

E

edge_mask (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) effective_coord (CyAtom attribute) effective_coords (Atoms property) effective_scene_coords (Atoms property) Element (class in chimerax.atomic.cymol) element (CyAtom attribute) element_names (Atoms property) element_numbers (Atoms property) ElementArg (class in chimerax.atomic.args) elements (Atoms property) Elements (class in chimerax.atomic.molarray) empty_drawing() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure 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)

ends_selected (Bond property) (Bonds property) enqueue() (FIFOHistory method) EnumBase (class in chimerax.ui.options.options) EnumOption (class in chimerax.ui.options.options) environment variable USERNAME, [1] error() (Logger method) estimate_assoc_params() (in module chimerax.atomic.molobject) evaluate() (AtomSpec method) everything() (in module chimerax.core.commands.atomspec) executable_dir() (BundleAPI static method) (BundleInfo method) execute() (PresetsManager method) existing_principal_atoms (Residues property) existing_residues (Chains property) (StructureSeq property) exit() (in module chimerax.std_commands.exit) EXPLICIT_SAVE (Settings attribute) extend() (Chain method) (CIFTable method) (FIFOHistory method) (Sequence method) eye_separation_pixels (StereoCamera attribute) eye_separation_scene (StereoCamera attribute)

F

fetch() (FetcherInfo method) fetch_args (FetcherInfo property) fetch_ccd() (in module chimerax.mmcif.mmcif) fetch_file() (in module chimerax.core.fetch) fetch_mmcif() (in module chimerax.mmcif.mmcif) fetch_pdb_redo() (in module chimerax.mmcif.mmcif) FetcherInfo (class in chimerax.open_command) field_has() (CIFTable method) field_of_view (MonoCamera attribute) (StereoCamera attribute) field_width (OrthographicCamera attribute) fields() (CIFTable method) 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) filter() (Collection method) find_atom() (CyResidue method) find_atoms() (Residues 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_existing_atoms() (Residues method) find_local_maxima() (in module chimerax.segment._segment) find_residue() (AtomicStructure method) (Structure method) (StructureData method)

find_template_residue() (in module chimerax.mmcif.mmcif) finish() (BundleAPI static method) (BundleInfo method) finish_rendering() (View method) first_intercept() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Model method) (MolecularSurface method) (PseudobondGroup method) (Structure method) first_intercept_children() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure 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) from_seqres (StructureSeq property) frustum() (in module chimerax.graphics.camera) full_region_on_gpu (RenderingOptions attribute) full_residues (Atoms property) full_sequence_known (StructureSeq property) full_structures (Atoms property)

G

gapped_to_ungapped() (Sequence method) gaussian_surface() (in module chimerax.surface.gaussian) gen_atom_name() (in module chimerax.atomic.struct_edit) geometry_bounds() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) get_alt_loc_coord() (CyAtom method) get_alt_loc_scene_coord() (CyAtom method) get_attribute() (Option method) get_cif_tables() (in module chimerax.mmcif.mmcif) get_class() (BundleAPI static method) (BundleInfo method) get_coordset_coord() (CyAtom method) get_coordset_scene_coord() (CyAtom method) get_element() (Element static method) get_group() (PseudobondManager method) get_mmcif_tables() (in module chimerax.mmcif.mmcif)

get_mmcif_tables_from_metadata() (in module chimerax.mmcif.mmcif) get_module() (BundleInfo method) get_num_pseudobonds() (PseudobondGroupData method) get_one_letter_code() (CyResidue method) get_pseudobonds() (PseudobondGroupData method) get_selected() (AtomicStructure method) (Model method) (PseudobondGroup method) (Structure method) get_selector() (in module chimerax.core.commands.atomspec) get_selector_description() (in module chimerax.core.commands.atomspec) get_standard_aa_name() (CyResidue static method) get_toolshed() (in module chimerax.core.toolshed) graphics() (in module chimerax.std_commands.graphics) grid_id (GridData attribute) GridData (class in chimerax.map_data) group (Pseudobond property) group_map (PseudobondManager property) group_type (PseudobondGroupData property) groups (Pseudobonds property)

H

half_colors (Bonds property) (Pseudobonds property) halfbond (Bond property) (Pseudobond property) (PseudobondGroupData property) halfbond_cylinder_placements() (Bonds method) halfbonds (Bonds property) (PseudobondGroupDatas property) (Pseudobonds property) has_alt_loc() (CyAtom method) has_aniso_u (Atoms property) has_field() (CIFTable method) has_formatted_metadata() (AtomicStructure method) (Model method) (Structure method) has_handlers() (TriggerSet method) has_selected_bonds (Atoms property) has_trigger() (TriggerSet method) hash() (Collection method) headerData() (QCxTableModel method) help (ToolInstance attribute) help() (in module chimerax.help_viewer.cmd) hidden_args (SaverInfo property) hide (Bond property) (CyAtom attribute) hide() (in module chimerax.std_commands.hide) (MolecularSurface method) hides (Atoms property) highlight_color (View property) HIGHLIGHT_DRAW_PASS (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute)

highlight_thickness (View property) highlighted (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) highlighted_displayed_triangles_mask (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) highlighted_positions (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) highlighted_triangles_mask (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure 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 (CoordSet property) (Model attribute) (Task attribute) id_string (AtomicStructure property) (Model property) (PickedTriangle property) (Structure property) idatm_failed (AtomicStructure property) (Structure property) (StructureData property) idatm_type (CyAtom attribute) idatm_types (Atoms property) idatm_valid (AtomicStructure property) (Structure property) (StructureData property) ideal_chirality() (Residue method) identity (Chain property) identity() (in module chimerax.geometry.place) ids (CoordSets property) ijk_to_xyz() (GridData method) image() (View method) image_mode (RenderingOptions attribute) image_rgba() (View method) import_bundle() (Toolshed method) in_chains (Atoms property) in_cycle (Bond property) in_file_history (FetcherInfo property) (OpenerInfo property) (SaverInfo property) include_dir() (BundleAPI static method) (BundleInfo method) INCLUDE_MAPS (AtomicStructure attribute) (LevelOfDetail attribute) (Structure attribute) include_state() (PseudobondManager method) index() (Collection method) indices() (Collection method) info() (in module chimerax.list_info.cmd) (Logger method) info_atomattr() (in module chimerax.list_info.cmd) info_atomcolor() (in module chimerax.list_info.cmd) info_bondattr() (in module chimerax.list_info.cmd) info_bounds() (in module chimerax.list_info.cmd) info_chains() (in module chimerax.list_info.cmd) info_distmat() (in module chimerax.list_info.cmd) info_models() (in module chimerax.list_info.cmd) info_path() (in module chimerax.list_info.cmd) info_polymers() (in module chimerax.list_info.cmd) info_resattr() (in module chimerax.list_info.cmd) info_rescolor() (in module chimerax.list_info.cmd) info_residues() (in module chimerax.list_info.cmd) info_selection() (in module chimerax.list_info.cmd) inherit_graphics_exemptions (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure 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) insertion_code (CyResidue attribute) insertion_codes (Residues property) install_bundle() (Toolshed method) installed (BundleInfo attribute) instances() (Collection method) 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() (AtomicStructure method) (Model method) (Structure method) intersect() (Collection method) intersects() (Collection method) intersects_each() (Collection method) IntOption (class in chimerax.ui.options.options) intra_bonds (Atoms property) inverse() (Place method) is_alkali_metal (Element attribute) (Elements property) is_backbone() (CyAtom method) is_blocked() (TriggerSet method) is_halogen (Element attribute) (Elements property) is_helices (Residues property) is_helix (CyResidue attribute) (Residues property) is_identity() (Place method) (Places method) is_informative_name() (in module chimerax.atomic.structure) is_metal (Element attribute) (Elements property) is_missing_heavy_template_atoms (Residues property) is_noble_gas (Element attribute) (Elements property) is_ribose (CyAtom attribute) is_riboses (Atoms property) is_selector_atomic() (in module chimerax.core.commands.atomspec) is_selector_user_defined() (in module chimerax.core.commands.atomspec) is_side_chain (CyAtom attribute) is_side_chains (Atoms property) is_side_connector (CyAtom attribute) is_side_connectors (Atoms property) is_side_only (CyAtom attribute) is_side_onlys (Atoms property) is_strand (CyResidue attribute) (Residues property) is_strands (Residues property) 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) label_one_letter_code (CyResidue attribute) label_specifier (CyResidue attribute) LabelHeightDialog (class in chimerax.ui.gui) largest_blobs_triangle_mask() (in module chimerax.surface.dust) LAST_DRAW_PASS (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) last_mouse_position (MouseMode attribute) length (Bond property) (Pseudobond property) lengths (Bonds property) (Pseudobonds property) lessThan() (NumSortingProxyModel method) level (VolumeSurface property) LEVEL_BUG (Log attribute) LEVEL_ERROR (Log attribute) LEVEL_INFO (Log attribute) LEVEL_WARNING (Log attribute) LevelOfDetail (class in chimerax.atomic.structure) 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) load_mmCIF_templates() (in module chimerax.mmcif.mmcif) 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) LookupTable (class in chimerax.atomic.molarray) lower() (CustomSortString method) lower_case_chains (AtomicStructure property) (Structure property) (StructureData property) (StructureDatas property) 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_elements_menu() (in module chimerax.atomic.widgets) make_link() (in module chimerax.core.utils) manage() (ToolWindow method) manual_block() (TriggerSet method) manual_release() (TriggerSet method) mapping() (CIFTable method) mask() (Collection method) (in module chimerax.mask.maskcommand) masked() (Places method) mass (Element attribute) masses (Elements property) Material (class in chimerax.graphics.opengl) material (View property) material() (in module chimerax.std_commands.material) matrix (Place property) matrix() (GridData method) maximum_bond_radii() (Atoms 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) measure_sasa() (in module chimerax.surface.measure_sasacmd) MenuButton (class in chimerax.ui.widgets.item_chooser) merge() (Collection method) Mesh (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) mesh_lighting (RenderingOptions attribute) metadata (AtomicStructure property) (Session attribute) (Structure property) (StructureData property) (StructureDatas property) migrate_from() (ConfigFile method) migrate_value() (ConfigFile method) minimal_texture_memory (RenderingOptions attribute) mlp() (in module chimerax.mlp.mlp) mmcif_chain_id (CyResidue attribute) mmcif_chain_ids (Residues property) 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.atomic.args chimerax.atomic.cymol chimerax.atomic.molarray chimerax.atomic.molobject chimerax.atomic.molsurf chimerax.atomic.pbgroup chimerax.atomic.struct_edit chimerax.atomic.structure chimerax.atomic.widgets 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.list_info.cmd chimerax.map.volume chimerax.map_series.vseries_command chimerax.mmcif.mmcif 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.dust chimerax.surface.gaussian 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

MolecularSurface (class in chimerax.atomic.molsurf) molecules (AtomicStructure property) (Structure property) (StructureData property) 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 (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) multitexture_reverse_order (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute)

N

name (Annotation attribute) (ArrayGridData attribute) (AtomicStructure property) (AtomsDrawing attribute) (BondsDrawing attribute) (BundleInfo property) (Camera attribute) (CyAtom attribute) (CyResidue attribute) (Drawing attribute) (Element attribute) (GridData attribute) (Model property) (MonoCamera attribute) (MouseMode attribute) (OrthographicCamera attribute) (PseudobondGroup property) (SaveFile attribute) (SelectorInfo attribute) (Sequence property) (SplitStereoCamera attribute) (StereoCamera attribute) (Structure property) (ToolInfo attribute) (Volume property) names (Atoms property) (Elements property) (PseudobondGroupDatas property) (PseudobondGroups property) (Residues property) natural_cubic_spline() (in module chimerax.geometry._geometry) near_far_distances() (View method) neighbors (Atoms property) (CyAtom attribute) (CyResidue attribute) new_atom() (AtomicStructure method) (Structure method) (StructureData method) new_bond() (AtomicStructure method) (Structure method) (StructureData method) new_coordset() (AtomicStructure method) (Structure method) (StructureData method) new_drawing() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) new_parameters() (MolecularSurface method) new_pseudobond() (PseudobondGroupData method) new_pseudobonds() (PseudobondGroupData method) new_region() (Volume method) new_residue() (AtomicStructure method) (Structure method) (StructureData method) newer_than() (BundleInfo method) NewerVersionQuery (class in chimerax.core.toolshed) nonstandard_residue_names (AtomicStructure property) (Structure property) (StructureData property) norm() (in module chimerax.geometry.vector) normalization() (Texture method) normalize_vector() (in module chimerax.geometry.vector) normalize_vectors() (in module chimerax.geometry.vector) normals (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property)

num_alt_locs (Atoms property) (CyAtom attribute) num_atoms (AtomicStructure property) (CyResidue attribute) (Residues property) (Structure property) (StructureData property) (StructureDatas property) num_atoms_visible (AtomicStructure property) (Structure property) (StructureData property) num_bonds (AtomicStructure property) (Atoms property) (CyAtom attribute) (Structure property) (StructureData property) (StructureDatas property) num_bonds_visible (AtomicStructure property) (Structure property) (StructureData property) num_chains (AtomicStructure property) (Structure property) (StructureData property) (StructureDatas property) num_coordsets (AtomicStructure property) (Structure property) (StructureData property) num_existing_residues (Chains property) (StructureSeq property) num_explicit_bonds (CyAtom attribute) num_pseudobonds (PseudobondGroupData property) (PseudobondGroupDatas property) num_residues (AtomicStructure property) (Atoms property) (Chains property) (Structure property) (StructureData property) (StructureDatas property) (StructureSeq property) num_ribbon_residues (AtomicStructure property) (Structure property) (StructureData property) num_rows() (CIFTable method) num_selected (Atoms property) (Bonds property) (Pseudobonds property) num_shown (Bonds property) number (CyResidue attribute) (Element attribute) number_of_positions() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) number_of_triangles() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) number_of_views() (Camera method) (SplitStereoCamera method) (StereoCamera method) numbers (Elements property) (Residues property) 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) occupancy (CyAtom attribute) octahedron_geometry() (in module chimerax.surface.shapes) omega (CyResidue attribute) on_disk() (ConfigFile method) on_finish() (NewerVersionQuery method) (Task method) on_top (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) ones_mask() (in module chimerax.mask.maskcommand) OPAQUE_DRAW_PASS (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) opaque_texture (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure 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) ordered_atoms (Ring property) ordered_bonds (Ring property) OrderedAtomsArg (class in chimerax.atomic.args) 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) other_atom() (Bond method) (Pseudobond method) outline_box_rgb (RenderingOptions attribute) OutputFileOption (class in chimerax.ui.options.options) OutputFolderOption (in module chimerax.ui.options.options) overall_color (AtomicStructure property) (Model property) (MolecularSurface property) (PseudobondGroup property) (Structure property) (Volume property) (VolumeImage property) overlays() (View method)

P

parse() (AtomArg class method) (AtomicStructureArg class method) (AtomicStructuresArg class method) (AtomsArg class method) (AtomSpecArg class method) (BondArg class method) (BondsArg class method) (ChainArg class method) (ElementArg class method) (OrderedAtomsArg class method) (PseudobondGroupsArg class method) (PseudobondsArg class method) (RawSequenceArg class method) (ResiduesArg class method) (SequenceArg class method) (SequencesArg class method) (SeriesArg class method) (StructureArg class method) (StructuresArg class method) (SymmetryArg static method) (UniProtIdArg class method) (UniProtSequenceArg class method) (UniqueChainsArg class method) PasswordOption (class in chimerax.ui.options.options) path (GridData attribute) pause() (MouseMode method) pb_coord (CyAtom attribute) pb_coords (Atoms property) pb_scene_coords (Atoms property) pbg_map (AtomicStructure property) (Structure property) (StructureData property) pbg_maps (StructureDatas property) pdb_version (AtomicStructure property) (Structure property) (StructureData property) 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) phi (CyResidue attribute) PhysicalSizeOption (class in chimerax.ui.options.options) Pick (class in chimerax.graphics.drawing) pickable (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) picked_object() (View method) picked_object_on_segment() (View method) PickedAtom (class in chimerax.atomic.structure) PickedAtoms (class in chimerax.atomic.structure) PickedBond (class in chimerax.atomic.structure) PickedBonds (class in chimerax.atomic.structure) PickedInstance (class in chimerax.graphics.drawing) PickedModel (class in chimerax.core.models) PickedPseudobond (class in chimerax.atomic.structure) PickedPseudobonds (class in chimerax.atomic.structure) PickedResidue (class in chimerax.atomic.structure) PickedResidues (class in chimerax.atomic.structure) 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() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (PseudobondGroup method) (Structure method) point_bounds() (in module chimerax.geometry.bounds) polymer_type (CyResidue attribute) (StructureSeq property) polymer_types (Chains property) (Residues property) polymers() (AtomicStructure method) (Structure method) (StructureData method) position (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Camera property) (Drawing property) (Model property) (PseudobondGroup property) (Structure property) position() (MouseEvent method) position_rgba_drawing() (in module chimerax.graphics.drawing) positions (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Model property) (PseudobondGroup property) (Structure property) PresetsManager (class in chimerax.preset_mgr.manager) principal_atom (CyResidue attribute) principal_atoms (Residues property) print() (CIFTable method) 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) Pseudobond (class in chimerax.atomic.molobject) pseudobond_group() (AtomicStructure method) (Structure method) (StructureData method) PseudobondGroup (class in chimerax.atomic.pbgroup) PseudobondGroupData (class in chimerax.atomic.molobject) PseudobondGroupDatas (class in chimerax.atomic.molarray) PseudobondGroups (class in chimerax.atomic.molarray) PseudobondGroupsArg (class in chimerax.atomic.args) PseudobondManager (class in chimerax.atomic.molobject) Pseudobonds (class in chimerax.atomic.molarray) pseudobonds (PseudobondGroupData property) (PseudobondGroupDatas property) PseudobondsArg (class in chimerax.atomic.args) psi (CyResidue attribute) 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

radii (Atoms property) (Bonds property) (PseudobondGroupDatas property) (Pseudobonds property) radius (Bond property) (CyAtom attribute) (Pseudobond property) (PseudobondGroupData property) radius() (Bounds method) rainbow() (in module chimerax.std_commands.rainbow) RawSequenceArg (class in chimerax.atomic.args) 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() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) Redust (class in chimerax.surface.dust) 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() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) remove_atom() (CyResidue method) remove_binding() (MouseModes method) remove_coordsets() (AtomicStructure method) (Structure method) (StructureData method) remove_drawing() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) remove_drawings() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) remove_handler() (TriggerSet method) remove_log() (Logger method) remove_mode() (MouseModes method) remove_overlays() (View method) remove_scale() (Place method) remove_solvent_ligands_ions() (in module chimerax.atomic.molsurf) 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) renumber_residues() (AtomicStructure method) (Structure method) (StructureData method) reorder_residues() (AtomicStructure method) (Structure method) (StructureData method) replace() (FIFOHistory method) report_exception() (Logger method) report_framerate() (View method) res_map (StructureSeq property) res_numbering (AtomicStructure property) (Structure property) (StructureData property) res_numbering_valid() (AtomicStructure method) (Structure method) (StructureData method) reset() (ConfigFile method) (Session method) (Settings method) reset_state() (Models method) (PseudobondManager method) (Tasks method) (Tools method) (UserAliases method) resfit() (in module chimerax.residue_fit.cmd) Residue (class in chimerax.atomic.molobject) residue (CyAtom attribute) residue_after() (StructureSeq method) residue_at() (StructureSeq method) residue_before() (StructureSeq method) residue_sums() (Atoms method) ResidueListWidget (class in chimerax.atomic.widgets) ResidueMenuButton (class in chimerax.atomic.widgets) residues (AtomicStructure property) (Atoms property) Residues (class in chimerax.atomic.molarray) residues (Structure property) (StructureData property) (StructureDatas property) (StructureSeq property) ResiduesArg (class in chimerax.atomic.args) resize() (View method) restore() (Session method) (Settings method) (Task method) restore_geometry() (AtomicStructure method) (Model method) (Structure method) restore_scene() (AtomicStructure method) (Model method) (Structure method) restore_snapshot() (Atom static method) (AtomicStructure static method) (Bond static method) (Chain static method) (Collection class method) (CoordSet static method) (LevelOfDetail static method) (Model class method) (Models static method) (MolecularSurface static method) (NewerVersionQuery class method) (Pseudobond static method) (PseudobondGroup static method) (PseudobondManager static method) (Redust class method) (Residue static method) (SeqMatchMap static method) (Sequence static method) (Structure static method) (StructureSeq static 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) ribbon_adjust (CyResidue attribute) ribbon_adjusts (Residues property) ribbon_color (CyResidue attribute) ribbon_colors (Residues property) ribbon_coord (CyAtom attribute) ribbon_coords (Atoms property) ribbon_display (CyResidue attribute) ribbon_display_count (AtomicStructure property) (Structure property) (StructureData property) ribbon_displays (Residues property) ribbon_hide_backbone (CyResidue attribute) ribbon_hide_backbones (Residues property) RIBBON_MODE_ARC (AtomicStructure attribute) (Structure attribute) (StructureData attribute) RIBBON_MODE_DEFAULT (AtomicStructure attribute) (Structure attribute) (StructureData attribute) ribbon_mode_helix (AtomicStructure property) (Structure property) (StructureData property) ribbon_mode_strand (AtomicStructure property) (Structure property) (StructureData property) RIBBON_MODE_WRAP (AtomicStructure attribute) (Structure attribute) (StructureData attribute) RIBBON_ORIENT_ATOMS (AtomicStructure attribute) (Structure attribute) (StructureData attribute) RIBBON_ORIENT_CURVATURE (AtomicStructure attribute) (Structure attribute) (StructureData attribute) RIBBON_ORIENT_GUIDES (AtomicStructure attribute) (Structure attribute) (StructureData attribute) RIBBON_ORIENT_PEPTIDE (AtomicStructure attribute) (Structure attribute) (StructureData attribute) ribbon_orientation (AtomicStructure property) (Structure property) (StructureData property) ribbon_orientations (StructureDatas property) ribbon_orients() (AtomicStructure method) (Structure method) (StructureData method) ribbon_show_spine (AtomicStructure property) (Structure property) (StructureData property) ribbon_show_spines (StructureDatas property) ribbon_tether_opacities (StructureDatas property) ribbon_tether_opacity (AtomicStructure property) (Structure property) (StructureData property) ribbon_tether_scale (AtomicStructure property) (Structure property) (StructureData property) ribbon_tether_scales (StructureDatas property) ribbon_tether_shape (AtomicStructure property) (Structure property) (StructureData property) ribbon_tether_shapes (StructureDatas property) ribbon_tether_sides (AtomicStructure property) (Structure property) (StructureData property) (StructureDatas property) Ring (class in chimerax.atomic.molobject) ring_color (CyResidue attribute) ring_colors (Residues property) ring_display (CyResidue attribute) ring_display_count (AtomicStructure property) (Structure property) (StructureData property) ring_displays (Residues property) Rings (class in chimerax.atomic.molarray) rings() (AtomicStructure method) (Bond method) (CyAtom method) (Structure method) (StructureData method) 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() (AtomicStructure method) (Model method) (Structure method) save_map() (in module chimerax.map.volume) save_pdb() (in module chimerax.pdb.pdb) save_state() (AtomicStructure method) (Structure method) (StructureData method) 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 (AtomicStructure attribute) (LevelOfDetail attribute) (Structure attribute) scene_bounds (Atoms property) scene_coord (CyAtom attribute) scene_coords (Atoms property) scene_position (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) scroll_to() (ItemTable method) sdump() (in module chimerax.core.session) search() (Sequence method) secondary_structure_ids (Residues property) 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) (PickedAtom method) (PickedAtoms method) (PickedBond method) (PickedBonds method) (PickedInstance method) (PickedModel method) (PickedPseudobond method) (PickedPseudobonds method) (PickedResidue method) (PickedResidues method) (PickedTriangle method) (PickedTriangles method) select_by_mode() (MainWindow method) selected (AtomicStructure property) (Atoms property) (Bond property) (Bonds property) (CyAtom attribute) (CyResidue attribute) (Model property) (MolecularSurface property) (Pseudobond property) (PseudobondGroup property) (Pseudobonds property) (Residues property) (Structure property) selected_atoms() (in module chimerax.atomic.structure) selected_bonds() (in module chimerax.atomic.structure) selected_chains() (in module chimerax.atomic.structure) selected_pseudobonds() (in module chimerax.atomic.pbgroup) selected_residues() (in module chimerax.atomic.structure) selecteds (Atoms property) SelectorInfo (class in chimerax.core.toolshed) SelSeqDialog (class in chimerax.ui.gui) SelZoneDialog (class in chimerax.ui.gui) SeqMatchMap (class in chimerax.atomic.molobject) Sequence (class in chimerax.atomic.molobject) SequenceArg (class in chimerax.atomic.args) SequencesArg (class in chimerax.atomic.args) serial_number (CyAtom attribute) serial_numbers (Atoms property) SeriesArg (class in chimerax.map_series.vseries_command) ses_surface_geometry() (in module chimerax.surface.gridsurf) SESSION (AtomicStructure attribute) session (Bond property) Session (class in chimerax.core.session) session (CoordSet property) (CyAtom attribute) SESSION (LevelOfDetail attribute) session (Pseudobond property) SESSION (Structure attribute) session (StructureSeq property) (Task property) (Tasks property) (ToolInstance property) (Volume attribute) session_atom_to_id() (AtomicStructure method) (Structure method) (StructureData method) session_bond_to_id() (AtomicStructure method) (Structure method) (StructureData method) session_chain_to_id() (AtomicStructure method) (Structure method) (StructureData method) SESSION_ENDURING (Model attribute) (Task attribute) (ToolInstance attribute) session_id_to_atom() (AtomicStructure method) (Structure method) (StructureData method) session_id_to_bond() (AtomicStructure method) (Structure method) (StructureData method) session_id_to_chain() (AtomicStructure method) (Structure method) (StructureData method) session_id_to_residue() (AtomicStructure method) (Structure method) (StructureData method) session_residue_to_id() (AtomicStructure method) (Structure method) (StructureData method) 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_alt_loc() (CyAtom method) (CyResidue method) set_attribute() (Option method) set_bonds() (Objects method) set_brightness() (VolumeSurface method) set_color() (AtomicStructure method) (Structure method) (StructureData 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() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) set_hide_bits() (Atoms method) (Bond method) (CyAtom method) set_linear_interpolation() (Texture method) set_metadata_entry() (AtomicStructure method) (Structure method) (StructureData method) (StructureDatas 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_res_numbering_valid() (AtomicStructure method) (Structure method) (StructureData method) set_rotation_depth() (View method) set_special_render_modes() (Camera method) set_state_from_snapshot() (AtomicStructure method) (Structure method) (StructureData method)

set_transparency() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure 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 (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure 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) (MolecularSurface method) (Volume method) show_metadata() (AtomicStructure method) (Model method) (Structure method) show_outline_box (RenderingOptions attribute) show_outline_box() (Volume method) show_text() (FloatOption method) (IntOption method) (NumericOption method) showing_transparent() (AtomicStructure method) (AtomsDrawing method) (BondsDrawing method) (Drawing method) (Structure method) shown (Bond property) (Pseudobond property) (ToolWindow property) shown_atoms (Atoms property) shown_changed() (ToolWindow method) shown_when_atoms_hidden (Pseudobond property) shown_when_atoms_hiddens (Pseudobonds property) showns (Bonds property) (Pseudobonds property) shrink_to_fit() (ToolWindow method) side_atoms() (Bond method) (CyAtom method) silhouette (View property) single_structure (Atoms property) size (GridData attribute) (Ring property) size() (Bounds method) (in module chimerax.std_commands.size) sizeHint() (HtmlView method) sizeHintForColumn() (ItemTable method) skew_axes() (in module chimerax.geometry.place) skip_bounds (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) smaller_side (Bond property) smooth_lines (RenderingOptions attribute) smoothing_factor (RenderingOptions attribute) smoothing_iterations (RenderingOptions attribute) smoothlines() (in module chimerax.smooth_lines.smoothlines) snapshot_methods() (Session method) Solid (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) specifier() (Pick method) (PickedAtom method) (PickedAtoms method) (PickedBond method) (PickedBonds method) (PickedModel method) (PickedPseudobond method) (PickedPseudobonds method) (PickedResidue method) (PickedResidues 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) split_volume_by_color_zone() (in module chimerax.surface.colorzone) SplitStereoCamera (class in chimerax.graphics.camera) square_mesh (RenderingOptions attribute) ss_assigned (AtomicStructure property) (Structure property) (StructureData property) ss_assigneds (StructureDatas property) ss_change_notifies (StructureDatas property) ss_change_notify (AtomicStructure property) (Structure property) (StructureData property) ss_id (CyResidue attribute) ss_ids (Residues property) ss_type (CyResidue attribute) ss_types (Residues property) standard_aa_name (CyResidue 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) string() (AtomicStructure method) (Bond method) (CyAtom method) (CyResidue method) (Pseudobond method) (Structure method) 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) StructAssocError structure (Bond property) Structure (class in chimerax.atomic.structure) structure (CoordSet property) (CyAtom attribute) (CyResidue attribute) (PseudobondGroupData property) (StructureSeq property) structure_atoms() (in module chimerax.atomic.structure) structure_categories (Atoms property) structure_category (CyAtom attribute) structure_residues() (in module chimerax.atomic.structure) StructureArg (class in chimerax.atomic.args) StructureData (class in chimerax.atomic.molobject) StructureDatas (class in chimerax.atomic.molarray) StructureListWidget (class in chimerax.atomic.widgets) StructureMenuButton (class in chimerax.atomic.widgets) structures (Atoms property) (Bonds property) (Chains property) Structures (class in chimerax.atomic.molarray) structures (CoordSets property) (Residues property) StructuresArg (class in chimerax.atomic.args) StructureSeq (class in chimerax.atomic.molobject) 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) subtract() (Collection method) suppress_ss_change_notifications() (AtomicStructure method) (Structure method) (StructureData method) Surface (class in chimerax.core.models) surface() (in module chimerax.surface.surfacecmds) surface_area() (in module chimerax.surface.area) surface_bounds() (Volume method) surface_cap() (in module chimerax.surface.surfacecmds) surface_close() (in module chimerax.surface.surfacecmds) surface_dust() (in module chimerax.surface.sop) surface_hide_patches() (in module chimerax.surface.surfacecmds) surface_show_patches() (in module chimerax.surface.surfacecmds) surface_smoothing (RenderingOptions attribute) surface_style() (in module chimerax.surface.surfacecmds) surface_undust() (in module chimerax.surface.sop) surface_unzone() (in module chimerax.surface.sop) surface_volume_and_area() (in module chimerax.surface.area) surface_zone() (in module chimerax.surface.sop) surfaces (Volume property) surfaces() (AtomicStructure method) (Structure method) sym() (in module chimerax.std_commands.sym) SymbolicEnumOption (class in chimerax.ui.options.options) symmetries (ArrayGridData attribute) (GridData attribute) SymmetryArg (class in chimerax.atomic.args) synopsis (BundleInfo property) (SelectorInfo attribute) (ToolInfo attribute)

T

TableMissingFieldsError take_snapshot() (Atom method) (AtomicStructure method) (Bond method) (Chain method) (Collection method) (CoordSet method) (LevelOfDetail method) (Model method) (Models method) (MolecularSurface method) (NewerVersionQuery method) (Pseudobond method) (PseudobondGroup method) (PseudobondManager method) (Redust method) (Residue method) (SeqMatchMap method) (Sequence method) (Structure method) (StructureSeq 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) TETHER_CONE (AtomicStructure attribute) (Structure attribute) (StructureData attribute) TETHER_CYLINDER (AtomicStructure attribute) (Structure attribute) (StructureData attribute) TETHER_REVERSE_CONE (AtomicStructure attribute) (Structure attribute) (StructureData attribute) tetrahedron_geometry() (in module chimerax.surface.shapes) text_image_rgba() (in module chimerax.graphics.drawing) texture (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) Texture (class in chimerax.graphics.opengl) texture (Drawing attribute) (Structure attribute) texture_coordinates (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) texture_format() (Texture method) thin_rings (CyResidue attribute) (Residues property) 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 (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) TRANSPARENT_DRAW_PASS (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) transpose() (Place method) triangle_mask (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) triangles (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) trigger_handlers() (TriggerSet method) trigger_names() (TriggerSet method) triggers (Session attribute) (Settings attribute) (Toolshed attribute) TriggerSet (class in chimerax.core.triggerset) try_assoc() (in module chimerax.atomic.molobject) 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) uncartoon() (in module chimerax.std_commands.cartoon) ungapped() (Sequence method) ungapped_to_gapped() (Sequence method) uninstall_bundle() (Toolshed method) union() (OrderedSet method) union_bounds() (in module chimerax.geometry.bounds) UniProtIdArg (class in chimerax.atomic.args) UniProtSequenceArg (class in chimerax.atomic.args) unique() (Collection method) unique_chain_ids (Atoms property) (Residues property) unique_chains (Residues property) unique_ids (Residues property) unique_names (Residues property) unique_ordered() (in module chimerax.atomic.molarray)

unique_residues (Atoms property) unique_sequences (Residues property) unique_structures (Atoms property) (Bonds property) (CoordSets property) (Pseudobonds property) (Residues property) UniqueChainsArg (class in chimerax.atomic.args) unload() (BundleInfo method) UnwantedCompressionError update() (ConfigFile method) (Settings method) update_ribbon_backbone_atom_visibility() (Atoms method) upper() (CustomSortString method) url (Annotation attribute) use_default_atom_radii() (AtomicStructure method) (Structure method) (StructureData method) use_default_radius() (CyAtom method) use_lighting (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure attribute) UserAliases (class in chimerax.core.session) USERNAME, [1] uses_wheel (MouseMode property)

V

valence (Element attribute) valences (Elements property) 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 (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure property) vertex_to_atom_map() (MolecularSurface method) vertices (AtomicStructure property) (AtomsDrawing property) (BondsDrawing property) (Drawing property) (Structure 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) visible (Bond property) (CyAtom attribute) visibles (Atoms property) (Bonds property) 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 (AtomicStructure attribute) (AtomsDrawing attribute) (BondsDrawing attribute) (Drawing attribute) (Structure 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) worm_radius (CyResidue attribute) worm_ribbon (AtomicStructure property) (Structure property) (StructureData property) worm_ribbons (StructureDatas property) writable() (SaveFile method) write() (SaveFile method) writelines() (SaveFile method)

X

xyz_max (Bounds attribute) xyz_min (Bounds attribute)

xyz_to_ijk() (GridData method) xyzs (CoordSet property)

Z

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

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