/
coot-gtk4.ui
15193 lines (14790 loc) · 701 KB
/
coot-gtk4.ui
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<?xml version="1.0" encoding="UTF-8"?>
<interface>
<requires lib="gtk" version="4.0"/>
<menu id="menubar">
<submenu>
<attribute name="label">File</attribute>
<section>
<item>
<attribute name="label">Open Coordinates...</attribute>
<attribute name="action">app.open_coordinates_action</attribute>
</item>
<item>
<attribute name="label">Auto Open MTZ...</attribute>
<attribute name="action">app.auto_open_mtz_action</attribute>
</item>
<item>
<attribute name="label">Open MTZ, mmCIF, fcf or phs...</attribute>
<attribute name="action">app.open_dataset_action</attribute>
</item>
<item>
<attribute name="label">Open Map...</attribute>
<attribute name="action">app.open_map_action</attribute>
</item>
<item>
<attribute name="label">Import CIF dictionary...</attribute>
<attribute name="action">app.import_cif_dictionary_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Get Monomer...</attribute>
<attribute name="action">app.get_monomer_action</attribute>
</item>
<item>
<attribute name="label">Search Monomer Library...</attribute>
<attribute name="action">app.search_monomer_library_action</attribute>
</item>
<item>
<attribute name="label">Fetch PDB using Accession Code...</attribute>
<attribute name="action">app.show_accession_code_fetch_frame</attribute>
<attribute name="target">oca</attribute>
</item>
<item>
<attribute name="label">Fetch PDB & Map using EDS...</attribute>
<attribute name="action">app.show_accession_code_fetch_frame</attribute>
<attribute name="target">eds</attribute>
</item>
<item>
<attribute name="label">Fetch PDB and Map Using PDB-REDO...</attribute>
<attribute name="action">app.show_accession_code_fetch_frame</attribute>
<attribute name="target">pdb-redo</attribute>
</item>
<item>
<attribute name="label">Fetch Corresponding AlphaFold Model & Superpose</attribute>
<attribute name="action">app.fetch_and_superpose_alphafold_models_action</attribute>
</item>
<item>
<attribute name="label">Fetch AlphaFold Model using Uniprot ID...</attribute>
<attribute name="action">app.show_accession_code_fetch_frame</attribute>
<attribute name="target">uniprot-id</attribute>
</item>
<item>
<attribute name="label">Fetch PDBe Ligand Description</attribute>
<attribute name="action">app.fetch_pdbe_ligand_description_action</attribute>
</item>
<item>
<attribute name="label">Fetch Map from EMDB...</attribute>
<attribute name="action">app.fetch_map_from_emdb_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Save Coordinates...</attribute>
<attribute name="action">app.save_coordinates_action</attribute>
</item>
<item>
<attribute name="label">Save Symmetry Coordinates...</attribute>
<attribute name="action">app.save_symmetry_coordinates_action</attribute>
</item>
<item>
<attribute name="label">Save State...</attribute>
<attribute name="action">app.save_state_action</attribute>
</item>
<item>
<attribute name="label">Recover Session...</attribute>
<attribute name="action">app.recover_session_action</attribute>
</item>
<item>
<attribute name="label">Export Map...</attribute>
<attribute name="action">app.file_export_map_action</attribute>
</item>
<item>
<attribute name="label">Export Map Fragment...</attribute>
<attribute name="action">app.file_export_map_fragment_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Delete Molecules and Maps...</attribute>
<attribute name="action">app.close_molecule_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Curlew...</attribute>
<attribute name="action">app.curlew_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Exit</attribute>
<attribute name="action">app.exit_action</attribute>
</item>
</section>
</submenu>
<submenu>
<attribute name="label">Edit</attribute>
<section>
<item>
<attribute name="label">Add Header Link...</attribute>
<attribute name="action">app.make_link_action</attribute>
</item>
<item>
<attribute name="label">Change Chain IDs...</attribute>
<attribute name="action">app.change_chain_ids_action</attribute>
</item>
<item>
<attribute name="label">Copy Molecule...</attribute>
<attribute name="action">app.copy_molecule_action</attribute>
</item>
<item>
<attribute name="label">Copy Fragment...</attribute>
<attribute name="action">app.copy_molecule_fragment_action</attribute>
</item>
<item>
<attribute name="label">Exchange Chain-IDs for Seg-IDs</attribute>
<attribute name="action">app.exchange_chain_ids_for_seg_ids_action</attribute>
</item>
<item>
<attribute name="label">Fix Nomenclature Errors...</attribute>
<attribute name="action">app.fix_nomenclature_errors_action</attribute>
</item>
<item>
<attribute name="label">Invert this Chiral Centre</attribute>
<attribute name="action">app.invert_this_chiral_centre_action</attribute>
</item>
<item>
<attribute name="label">Merge Molecules...</attribute>
<attribute name="action">app.merge_molecules_action</attribute>
</item>
<item>
<attribute name="label">Merge Water Chains...</attribute>
<attribute name="action">app.merge_solvent_chains_action</attribute>
</item>
<item>
<attribute name="label">Move Molecule Here...</attribute>
<attribute name="action">app.move_molecule_here_action</attribute>
</item>
<item>
<attribute name="label">Mutate Residue Range...</attribute>
<attribute name="action">app.mutate_molecule_action</attribute>
</item>
<item>
<attribute name="label">Replace Fragment...</attribute>
<attribute name="action">app.edit_replace_fragment_action</attribute>
</item>
<item>
<attribute name="label">Replace Residue...</attribute>
<attribute name="action">app.edit_replace_residue_action</attribute>
</item>
<item>
<attribute name="label">Renumber Residues...</attribute>
<attribute name="action">app.renumber_residues_action</attribute>
</item>
<item>
<attribute name="label">Renumber Waters</attribute>
<attribute name="action">app.renumber_waters_action</attribute>
</item>
<item>
<attribute name="label">Residue Info</attribute>
<attribute name="action">app.residue_info_action</attribute>
</item>
<item>
<attribute name="label">Restraints...</attribute>
<attribute name="action">app.edit_restraints_action</attribute>
</item>
<item>
<attribute name="label">Undo Molecule Chooser...</attribute>
<attribute name="action">app.undo_molecule_chooser_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Preferences...</attribute>
<attribute name="action">app.show_preferences_action</attribute>
</item>
<item>
<attribute name="label">Shader Preferences...</attribute>
<attribute name="action">app.show_shader_preferences_action</attribute>
</item>
<submenu>
<attribute name="label">Settings...</attribute>
<section>
<submenu>
<attribute name="label">Rotate/Translate Zone Mode...</attribute>
<section>
<item>
<attribute name="label">Rotate about Zone Centre</attribute>
</item>
<item>
<attribute name="label">Rotate about Second-clicked Atom</attribute>
</item>
</section>
</submenu>
<item>
<attribute name="label">Set Spin Speed...</attribute>
</item>
<item>
<attribute name="label">Nudge Centre...</attribute>
</item>
<item>
<attribute name="label">All Molecules use "Near Chains" Symmetry</attribute>
</item>
<item>
<attribute name="label">Save Graphics Window Size and Position</attribute>
</item>
<item>
<attribute name="label">Enable Quick-Save Checkpointing</attribute>
</item>
</section>
</submenu>
</section>
</submenu>
<submenu>
<attribute name="label">Calculate</attribute>
<section>
<item>
<attribute name="label">Align and Mutate...</attribute>
<attribute name="action">app.align_and_mutate_action</attribute>
</item>
<submenu>
<attribute name="label">Assign Sequence...</attribute>
<item>
<attribute name="label">1: Associate Sequence File...</attribute>
<attribute name="action">app.associate_sequence_file_action</attribute>
</item>
<item>
<attribute name="label">2: Assign Sequence</attribute>
<attribute name="action">app.assign_sequence_action</attribute>
</item>
</submenu>
<submenu>
<attribute name="label">Fit Loop...</attribute>
<item>
<attribute name="label">Fit Loop by Database Search...</attribute>
<attribute name="action">app.fit_loop_by_database_search</attribute>
</item>
<item>
<attribute name="label">Fit Loop by Ramachandran Search...</attribute>
<attribute name="action">app.fit_loop_by_ramachandran_search</attribute>
</item>
</submenu>
<item>
<attribute name="label">Hydrogen Bonds</attribute>
<attribute name="action">app.calculate_hydrogen_bonds_action</attribute>
</item>
<item>
<attribute name="label">Load Tutorial Model & Data</attribute>
<attribute name="action">app.load_tutorial_model_and_data_action</attribute>
</item>
<item>
<attribute name="label">Ligand Builder...</attribute>
<attribute name="action">app.ligand_builder_action</attribute>
</item>
<item>
<attribute name="label">LSQ Superpose...</attribute>
<attribute name="action">app.lsq_superpose_action</attribute>
</item>
<submenu>
<attribute name="label">Map Tools...</attribute>
<section>
<item>
<attribute name="label">Mask Map by Atom Selection...</attribute>
<attribute name="action">app.mask_map_by_atom_selection_action</attribute>
</item>
<item>
<attribute name="label">Copy Map...</attribute>
<attribute name="action">app.copy_map_action</attribute>
</item>
<item>
<attribute name="label">Make a Smoother Copy...</attribute>
<attribute name="action">app.make_a_smoother_copy_of_a_map_action</attribute>
</item>
<item>
<attribute name="action">app.make_a_very_smooth_copy_of_a_map_action</attribute>
<attribute name="label">Make a Very Smooth Copy</attribute>
</item>
<item>
<attribute name="label">Make a Difference Map...</attribute>
<attribute name="action">app.make_a_difference_map_action</attribute>
</item>
<item>
<attribute name="label">Transform Map by LSQ Model Fit...</attribute>
<attribute name="action">app.transform_map_by_lsq_model_fit_action</attribute>
</item>
<item>
<attribute name="label">Average Maps...</attribute>
<attribute name="action">app.average_maps_action</attribute>
</item>
<item>
<attribute name="label">Map Density Histogram [Placeholder]</attribute>
</item>
<item>
<attribute name="label">Brighten Maps...</attribute>
<attribute name="action">app.brighten_maps_action</attribute>
</item>
<item>
<attribute name="label">Set Map is Difference Map...</attribute>
<attribute name="action">app.set_map_is_difference_map_action</attribute>
</item>
<item>
<attribute name="label">Another Contour Level</attribute>
<attribute name="action">app.another_contour_level_action</attribute>
</item>
<item>
<attribute name="label">Multi-Chicken...</attribute>
<attribute name="action">app.multichicken_action</attribute>
</item>
</section>
</submenu>
<item>
<attribute name="label">x-ray Map Sharpening/Blurring...</attribute>
<attribute name="action">app.sharpen_blur_for_xray_action</attribute>
</item>
<!-- remove skeleton for now -->
<!-- <item> -->
<!-- <attribute name="label">Map Skeleton...</attribute> -->
<!-- </item> -->
<item>
<attribute name="label">Run Script...</attribute>
<attribute name="action">app.run_script_action</attribute>
</item>
<submenu>
<attribute name="label">Scripting...</attribute>
<item>
<attribute name="label">Python...</attribute>
<attribute name="action">app.scripting_python_action</attribute>
</item>
<item>
<attribute name="label">Scheme</attribute>
</item>
</submenu>
<item>
<attribute name="label">SSM Superpose...</attribute>
<attribute name="action">app.ssm_superposition_action</attribute>
</item>
<item>
<attribute name="label">Superpose Ligands...</attribute>
<attribute name="action">app.superpose_ligands_action</attribute>
</item>
<item>
<attribute name="label">Updating Maps...</attribute>
<attribute name="action">app.calculate_updating_maps_action</attribute>
</item>
<item>
<attribute name="label">Use ClustalW for Alignment then Mutate</attribute>
<attribute name="action">app.use_clustalw_for_alignment_then_mutate_action</attribute>
</item>
</section>
</submenu>
<submenu>
<attribute name="label">Modelling</attribute>
<item>
<attribute name="label">Add An Atom</attribute>
<attribute name="action">app.add_an_atom_action</attribute>
</item>
<item>
<attribute name="label">Add Hydrogen Atoms</attribute>
<attribute name="action">app.add_hydrogen_atoms_action</attribute>
</item>
<item>
<attribute name="label">Add Hydrogen Atoms Using REFMAC</attribute>
<attribute name="action">app.add_hydrogen_atoms_using_refmac_action</attribute>
</item>
<item>
<attribute name="label">Add Other Solvent Molecules...</attribute>
<attribute name="action">app.add_other_solvent_molecules_action</attribute>
</item>
<item>
<attribute name="label">Add OXT to residue...</attribute>
<attribute name="action">app.add_OXT_to_residue_action</attribute>
</item>
<item>
<attribute name="label">Arrange Waters Around Protein</attribute>
<attribute name="action">app.arrange_waters_around_protein_action</attribute>
</item>
<item>
<attribute name="label">Assign (Force) HETATMs for this Residue</attribute>
<attribute name="action">app.assign_hetatms_for_this_residue_action</attribute>
</item>
<item>
<attribute name="label">Assign HETATMs to Molecule...</attribute>
<attribute name="action">app.assign_hetatoms_to_molecule_action</attribute>
</item>
<item>
<attribute name="label">Backrub Rotamers for Chain</attribute>
<attribute name="action">app.backrub_rotamers_for_chain_action</attribute>
</item>
<item>
<attribute name="label">cis ↔ trans</attribute>
<attribute name="action">app.cis_trans_convert_action</attribute>
</item>
<item>
<attribute name="label">DNA/RNA Models...</attribute>
<attribute name="action">app.dna_rna_models_action</attribute>
</item>
<item>
<attribute name="label">Find Ligands...</attribute>
<attribute name="action">app.find_ligands_action</attribute>
</item>
<item>
<attribute name="label">Find Waters...</attribute>
<attribute name="action">app.find_waters_action</attribute>
</item>
<submenu>
<attribute name="label">Find Secondary Structure in Map...</attribute>
<item>
<attribute name="label">Find Helices</attribute>
<attribute name="action">app.find_helices_in_map_action</attribute>
</item>
<item>
<attribute name="label">Find Strands</attribute>
<attribute name="action">app.find_strands_in_map_action</attribute>
</item>
</submenu>
<item>
<attribute name="label">Fill Partial Residues</attribute>
<attribute name="action">app.fill_partial_residues_action</attribute>
</item>
<submenu>
<attribute name="label">NCS Model Tools...</attribute>
<item>
<attribute name="label">Copy NCS Residue Range</attribute>
<attribute name="action">app.copy_ncs_residue_range_action</attribute>
</item>
<item>
<attribute name="label">Copy NCS Chain...</attribute>
<attribute name="action">app.copy_ncs_chain_action</attribute>
</item>
<!-- <item> -->
<!-- <attribute name="label">Copy NCS Ghosts by Residue Range...</attribute> -->
<!-- <attribute name="action">app.copy_ncs_ghosts_by_residue_range_action</attribute> -->
<!-- </item> -->
<item>
<attribute name="label">NCS Jumping...</attribute>
<attribute name="action">app.ncs_jumping_action</attribute>
</item>
<item>
<attribute name="label">NCS Ligands...</attribute>
<attribute name="action">app.ncs_ligands_action</attribute>
</item>
</submenu>
<item>
<attribute name="label">Phosphorylate This Residue</attribute>
<attribute name="action">app.phosphorylate_this_residue_action</attribute>
</item>
<item>
<attribute name="label">Place Helix Here</attribute>
<attribute name="action">app.place_helix_here_action</attribute>
</item>
<item>
<attribute name="label">Rebuild Fragment using DBLoop (Small)</attribute>
<attribute name="action">app.rebuild_fragment_using_dbloop_action</attribute>
<attribute name="target">small</attribute>
</item>
<item>
<attribute name="label">Rebuild Fragment using DBLoop (Bigger)</attribute>
<attribute name="action">app.rebuild_fragment_using_dbloop_action</attribute>
<attribute name="target">bigger</attribute>
</item>
<item>
<attribute name="label">Replace Residue</attribute>
<attribute name="action">app.replace_residue_action</attribute>
</item>
<item>
<attribute name="label">Reverse Chain Direction</attribute>
<attribute name="action">app.reverse_chain_direction_action</attribute>
</item>
<item>
<attribute name="label">Rigid-Body Fit Residue Ranges</attribute>
<attribute name="action">app.rigid_body_fit_residue_ranges_action</attribute>
</item>
<item>
<attribute name="label">Rigid-Body Fit Molecule</attribute>
<attribute name="action">app.rigid_body_fit_molecule_action</attribute>
</item>
<item>
<attribute name="label">Superpose Ligand</attribute>
<attribute name="action">app.superpose_ligands_action</attribute>
</item>
<item>
<attribute name="label">Symm Shift Reference Chain Here</attribute>
<attribute name="action">app.symm_shift_reference_chain_here_action</attribute>
</item>
<item>
<attribute name="label">What's This?</attribute>
<attribute name="action">app.whats_this_action</attribute>
</item>
</submenu>
<submenu>
<attribute name="label">Draw</attribute>
<submenu>
<attribute name="label">View</attribute>
<section>
<!-- <item> -->
<!-- <attribute name="label">Background Colour...</attribute> -->
<!-- <attribute name="action">app.background_colour_action</attribute> -->
<!-- </item> -->
<submenu>
<attribute name="label">Background Colour...</attribute>
<item>
<attribute name="label">Black</attribute>
<attribute name="action">app.background_black_action</attribute>
</item>
<item>
<attribute name="label">Dark Grey</attribute>
<attribute name="action">app.background_dark_grey_action</attribute>
</item>
<item>
<attribute name="label">Light Grey</attribute>
<attribute name="action">app.background_light_grey_action</attribute>
</item>
<item>
<attribute name="label">White</attribute>
<attribute name="action">app.background_white_action</attribute>
</item>
</submenu>
<item>
<attribute name="label">Display Only Active</attribute>
<attribute name="action">app.display_only_active_action</attribute>
</item>
<item>
<attribute name="label">Frames/Sec...</attribute>
<attribute name="action">app.toggle_display_frames_per_second_action</attribute>
</item>
<item>
<attribute name="label">Fullscreen</attribute>
<attribute name="action">app.fullscreen_action</attribute>
</item>
<item>
<attribute name="label">Generic Display Objects...</attribute>
<attribute name="action">app.generic_objects_action</attribute>
</item>
<section>
<submenu>
<attribute name="label">Projection...</attribute>
<item>
<attribute name="label">Orthographic</attribute>
<attribute name="action">app.orthographic_view_action</attribute>
</item>
<item>
<attribute name="label">Perspective</attribute>
<attribute name="action">app.perspective_view_action</attribute>
</item>
</submenu>
</section>
<item>
<attribute name="label">Screenshot</attribute>
<attribute name="action">app.screenshot_action</attribute>
</item>
<item>
<attribute name="label">Spin View</attribute>
<attribute name="action">app.spin_view_action</attribute>
</item>
<item>
<attribute name="label">Rock View</attribute>
<attribute name="action">app.rock_view_action</attribute>
</item>
<item>
<attribute name="label">Undo Last Navigation</attribute>
<attribute name="action">app.undo_last_navigation_action</attribute>
</item>
<item>
<attribute name="label">Undo Symmetry View</attribute>
<attribute name="action">app.undo_symmetry_view_action</attribute>
</item>
</section>
</submenu>
<submenu>
<attribute name="label">Molecule</attribute>
<section>
<item>
<attribute name="label">Bond Colours...</attribute>
<attribute name="action">app.bond_colours_action</attribute>
</item>
<item>
<attribute name="label">Bond Parameters...</attribute>
<attribute name="action">app.bond_parameters_action</attribute>
</item>
<submenu>
<attribute name="label">Carbon Colours</attribute>
<item>
<attribute name="label">Grey Carbon Colours</attribute>
<attribute name="action">app.grey_carbon_colours</attribute>
</item>
<item>
<attribute name="label">Coloured Carbon Colours</attribute>
<attribute name="action">app.coloured_carbon_colours</attribute>
</item>
</submenu>
<!-- this does not belong here - move this configuration into preferences -->
<!-- <item> -->
<!-- <attribute name="label">Centre Atom Label...</attribute> -->
<!-- <attribute name="action">app.on_draw_cente__action</attribute> -->
<!-- </item> -->
<item>
<attribute name="label">Cell & Symmetry...</attribute>
<attribute name="action">app.draw_cell_and_symmetry_action</attribute>
</item>
<!-- this does not belong here - move this configuration into preferences -->
<!-- <item> -->
<!-- <attribute name="label">Central Atom Label...</attribute> -->
<!-- <attribute name="action">app.draw_central_atom_label_action</attribute> -->
<!-- </item> -->
<item>
<attribute name="label">Go To Atom...</attribute>
<attribute name="action">app.go_to_atom_action</attribute>
</item>
<item>
<attribute name="label">Label Atoms in Residue</attribute>
<attribute name="action">app.label_atoms_in_residue_action</attribute>
</item>
<item>
<attribute name="label">Label CAs</attribute>
<attribute name="action">app.label_CA_atoms_action</attribute>
</item>
<item>
<attribute name="label">Label Neighbours</attribute>
<attribute name="action">app.label_neighbours_action</attribute>
</item>
<item>
<attribute name="label">Map Parameters...</attribute>
<attribute name="action">app.map_parameters_action</attribute>
</item>
<item>
<attribute name="label">NCS Ghost Control...</attribute>
<attribute name="action">app.ghost_control_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Residue Type Selection</attribute>
<attribute name="action">app.residue_type_selection_action</attribute>
</item>
<item>
<attribute name="label">Residues With Alt Confs...</attribute>
<attribute name="action">app.residues_with_alt_confs_action</attribute>
</item>
<item>
<attribute name="label">Residues With cis-Peptides...</attribute>
<attribute name="action">app.residues_with_cis_peptides_action</attribute>
</item>
<item>
<attribute name="label">Residues With Missing Atoms...</attribute>
<attribute name="action">app.residues_with_missing_atoms_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Ribbons: By Chain</attribute>
<attribute name="action">app.ribbons_colour_by_chain_action</attribute>
</item>
<item>
<attribute name="label">Ribbons: Rainbow</attribute>
<attribute name="action">app.ribbons_colour_rainbow_action</attribute>
</item>
<item>
<attribute name="label">Ribbons: Sec. Struct.</attribute>
<attribute name="action">app.ribbons_colour_by_secondary_structure_action</attribute>
</item>
</section>
<section>
<item>
<attribute name="label">Sequence View</attribute>
<attribute name="action">app.sequence_view_action</attribute>
</item>
<!-- reactivate this one day hopefully -->
<!-- <item> -->
<!-- <attribute name="label">Stereo...</attribute> -->
<!-- </item> -->
</section>
</submenu>
</submenu>
<submenu>
<attribute name="label">Measures</attribute>
<section>
<item>
<attribute name="label">Clear Atom Labels</attribute>
<attribute name="action">app.clear_atom_labels_action</attribute>
</item>
<item>
<attribute name="label">Distances & Angles...</attribute>
<attribute name="action">app.distances_and_angles_action</attribute>
</item>
<item>
<attribute name="label">Environment Distances...</attribute>
<attribute name="action">app.environment_distances_action</attribute>
</item>
<item>
<attribute name="label">Residue Info...</attribute>
<attribute name="action">app.residue_info_action</attribute>
</item>
<!-- reactivate this one day -->
<!-- <item> -->
<!-- <attribute name="label">Plane Distances...</attribute> -->
<!-- <attribute name="action">app.plane_distances_action</attribute> -->
<!-- </item> -->
<item>
<attribute name="label">Pointer Distances...</attribute>
<attribute name="action">app.pointer_distances_action</attribute>
</item>
</section>
</submenu>
<submenu>
<attribute name="label">Validate</attribute>
<section>
<item>
<attribute name="label">Validation graphs</attribute>
<attribute name="action">app.show_validation_graphs_dialog</attribute>
</item>
<item>
<attribute name="label">Ramachandran Plot</attribute>
<attribute name="action">app.ramachandran_plot_action</attribute>
</item>
<item>
<attribute name="label">Alignment vs Reference PIR</attribute>
<attribute name="action">app.alignment_vs_pir_action</attribute>
</item>
<item>
<attribute name="label">Atoms with Zero Occupancies...</attribute>
<attribute name="action">app.atoms_with_zero_occupancies_action</attribute>
</item>
<item>
<attribute name="label">Atom Overlaps</attribute>
<attribute name="action">app.atoms_overlaps_action</attribute>
</item>
<item>
<attribute name="label">Atom-Atom Contact Dots (Molprobity)</attribute>
<attribute name="action">app.all_atom_contact_dots_molprobity_action</attribute>
</item>
<item>
<attribute name="label">Check/Delete Waters...</attribute>
<attribute name="action">app.check_delete_waters_action</attribute>
</item>
<item>
<attribute name="label">Difference Map Peaks...</attribute>
<attribute name="action">app.difference_map_peaks_action</attribute>
</item>
<item>
<attribute name="label">Highly Coordinated Waters</attribute>
<attribute name="action">app.highly_coordinates_waters_action</attribute>
</item>
<!-- restore this one day -->
<!-- <item> -->
<!-- <attribute name="label">Kleywegt Plot...</attribute> -->
<!-- <attribute name="action">app.on_undo_symmetry_view1_action</attribute> -->
<!-- </item> -->
<item>
<attribute name="label">Overlaps, Peptides, CBeta, Rama & Rota Outliers</attribute>
<attribute name="action">app.overlaps_peptides_cbeta_ramas_and_rotas_action</attribute>
</item>
<item>
<attribute name="label">Pepflips from Difference Map...</attribute>
<attribute name="action">app.pepflips_from_difference_map_action</attribute>
</item>
<item>
<attribute name="label">Refmac Log Validation</attribute>
<attribute name="action">app.refmac_log_validation_action</attribute>
</item>
<item>
<attribute name="label">Unmodelled blobs...</attribute>
<attribute name="action">app.unmodelled_blobs_action</attribute>
</item>
<item>
<attribute name="label">Validation Outliers</attribute>
<attribute name="action">app.validation_outliers_action</attribute>
</item>
</section>
</submenu>
<submenu>
<attribute name="label">About</attribute>
<section>
<item>
<attribute name="label">About Coot...</attribute>
<attribute name="action">app.about_coot_action</attribute>
</item>
<item>
<attribute name="label">Header/Remarks Browser...</attribute>
<attribute name="action">app.remarks_browser_action</attribute>
</item>
</section>
</submenu>
</menu>
<menu id="refine-menu">
<section>
<item>
<attribute name="label" translatable="yes">RSR Sphere</attribute>
<attribute name="action">app.refine_sphere</attribute>
</item>
<item>
<attribute name="label" translatable="yes">RSR Big Sphere</attribute>
<attribute name="action">app.refine_sphere_big</attribute>
</item>
<item>
<attribute name="label" translatable="yes">RSR Tandem ± 3</attribute>
<attribute name="action">app.refine_tandem_3</attribute>
</item>
<item>
<attribute name="label" translatable="yes">RSR Tandem ± 5</attribute>
<attribute name="action">app.refine_tandem_5</attribute>
</item>
<item>
<attribute name="label" translatable="yes">RSR Single Residue</attribute>
<attribute name="action">app.refine_single_residue</attribute>
</item>
<item>
<attribute name="label" translatable="yes">RSR Chain</attribute>
<attribute name="action">app.refine_chain</attribute>
</item>
<item>
<attribute name="label" translatable="yes">RSR All Atoms</attribute>
<attribute name="action">app.refine_all_atoms</attribute>
</item>
<item>
<attribute name="label" translatable="yes">RSR Range Refine</attribute>
<attribute name="action">app.refine_range</attribute>
</item>
<item>
<attribute name="label" translatable="yes">RSR Repeat Range Refine</attribute>
<attribute name="action">app.repeat_refine_range</attribute>
</item>
</section>
<section>
<item>
<attribute name="label" translatable="yes">Regularize Sphere</attribute>
<attribute name="action">app.refine_regularize_sphere</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Regularize Tandem ± 3</attribute>
<attribute name="action">app.refine_regularize_tandem_3</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Regularize Single Residue</attribute>
<attribute name="action">app.refine_regularize_single_residue</attribute>
</item>
</section>
</menu>
<menu id="modules-menu">
<section>
<item>
<attribute name="label">CCP4</attribute>
<attribute name="action">app.add_ccp4_module_action</attribute>
</item>
<!-- remove the carbohydrate modules for now -->
<!-- <item> -->
<!-- <attribute name="label">Carbohydrate</attribute> -->
<!-- <attribute name="action">app.add_carbohydrate_module_action</attribute> -->
<!-- </item> -->
<item>
<attribute name="label">Cryo-EM</attribute>
<attribute name="action">app.add_cryo_em_module_action</attribute>
</item>
<item>
<attribute name="label">HOLE</attribute>
<attribute name="action">app.add_HOLE_module_action</attribute>
</item>
<item>
<attribute name="label">Ligand</attribute>
<attribute name="action">app.add_ligand_module_action</attribute>
</item>
<item>
<attribute name="label">ProSMART</attribute>
<attribute name="action">app.add_prosmart_module_action</attribute>
</item>
<item>
<attribute name="label">RCrane</attribute>
<attribute name="action">app.add_rcrane_module_action</attribute>
</item>
<item>
<attribute name="label">Restraints</attribute>
<attribute name="action">app.add_restraints_module_action</attribute>
</item>
<item>
<attribute name="label">Refine</attribute>
<attribute name="action">app.add_refine_module_action</attribute>
</item>
<item>
<attribute name="label">SHELX</attribute>
<attribute name="action">app.add_shelx_module_action</attribute>
</item>
<item>
<attribute name="label">Views</attribute>
<attribute name="action">app.add_views_module_action</attribute>
</item>
</section>
</menu>
<menu id="fixed-atoms-menu">
<section>
<item>
<attribute name="label" translatable="yes">Fix Atom</attribute>
<attribute name="action">app.fix_atom</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Unfix Atom</attribute>
<attribute name="action">app.unfix_atom</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Unfix All Atoms</attribute>
<attribute name="action">app.unfix_all_atoms</attribute>
</item>
</section>
</menu>
<menu id="rotate-translate-menu">
<section>
<item>
<attribute name="label" translatable="yes">Atom</attribute>
<attribute name="action">app.rotate_translate_atom</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Residue</attribute>
<attribute name="action">app.rotate_translate_residue</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Residue Range</attribute>
<attribute name="action">app.rotate_translate_residue_range</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Chain</attribute>
<attribute name="action">app.rotate_translate_chain</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Molecule</attribute>
<attribute name="action">app.rotate_translate_molecule</attribute>
</item>
</section>
</menu>
<menu id="delete-item-menu">
<section>
<item>
<attribute name="label" translatable="yes">Atom</attribute>
<attribute name="action">app.delete_item</attribute>
<attribute name="target">atom</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Water</attribute>
<attribute name="action">app.delete_item</attribute>
<attribute name="target">water</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Side-chain</attribute>
<attribute name="action">app.delete_item</attribute>
<attribute name="target">side-chain</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Side-chains in Residue Range</attribute>
<attribute name="action">app.delete_item</attribute>
<attribute name="target">side-chain-residue-range</attribute>
</item>
<item>
<attribute name="label" translatable="yes">Side-chains in Chain</attribute>
<attribute name="action">app.delete_item</attribute>
<attribute name="target">side-chains-in-chain</attribute>
</item>
<item>