Index for PHENIX web site

• 2fofcwt_no_fill
  • refinement.htm (mtz_label_amplitudes_3)
• abnormalities
  • xtriage.htm (interpreting_xtriage_output_2)
• abs_fcalc
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (output)
• absence
  • pdbtools.htm (anch1)
• absent
  • validation.htm (running_validation_2)
  • validation.htm (all-atom_contacts_2)
• absent_atom_type
  • refinement.htm (absent_atom_type)
• absolute_angle_tolerance
  • explore_metric_symmetry.htm (keywords_2)
• absorption
  • autosol.htm (datafile_formats_in_autosol_4)
• acceptable_cc_hyss
  • autosol.htm (acceptable_cc_hyss)
  • autosol.htm (n_add_res_max)
  • autosol.htm (add_res_max)
• acceptable_quality
  • autosol.htm (acceptable_quality)
• acceptable_r
  • autobuild.htm (acceptable_r)
• acceptable_secondary_structure_cc
  • autosol.htm (acceptable_secondary_structure_cc)
  • tutorial_mir.htm (model-building_with_resolve_2)
  • tutorial_mad.htm (model-building_with_resolve_2)
  • tutorial_sad.htm (model-building_with_resolve_2)
• acentric
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_sad.htm (final_phasing_with_phaser_2)
  • tutorial_twin.htm (examples_2)
• add_d_to_water
  • ready_set.htm (add_d_to_water)
• add_extra_if_fa
  • autosol.htm (add_extra_if_fa)
• add_h
  • pdbtools.htm (anch1)
• add_h_to_water
  • refinement.htm (hydrogens_in_refinement_2)
  • ready_set.htm (add_h_to_water)
• add_hydrogens
  • refinement.htm (add_hydrogens)
• add_res_max
  • autosol.htm (acceptable_cc_hyss)
  • autosol.htm (n_add_res_max)
  • autosol.htm (add_res_max)
• add_sidechains
  • autosol.htm (add_sidechains)
• add_sigmas
  • pdbtools.htm (add_sigmas)
• added_component
  • automr.htm (added_component)
• added_deriv
  • autosol.htm (added_deriv)
• added_ensemble
  • automr.htm (added_ensemble)
• added_native
  • autosol.htm (added_native)
• added_wavelength
  • autosol.htm (added_wavelength)
  • tutorial_mad.htm (summary_of_the_command-line_arguments_4)
  • tutorial_mad.htm (summary_of_the_command-line_arguments_5)
• adjacent
  • validation.htm (validation_of_protein_geometry_2)
• adp_restraints
  • refinement.htm (eps)
• after_autosol
  • faqs.htm
  • faqs.htm
  • autobuild.htm (run_autobuild_automatically_after_autosol_2)
  • autobuild.htm (seq_file)
  • autobuild.htm (map_file)
• algebraic
  • refinement.htm (refinement_using_twinned_data_2)
  • refinement.htm (mode_5)
  • tutorial_twin.htm (background_and_nomenclature_6)
  • tutorial_twin.htm (map_inspection_2)
• align
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__6)
  • find_helices_strands.htm (standard_run_of_find_helices_strands__3)
• alignment_style
  • superpose_pdbs.htm (alignment_style)
• aligns
  • tutorial_mir.htm
• all_harmonic
  • refinement.htm (dihedral_function_type)
  • pdbtools.htm (dihedral_function_type)
• all_ligands
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
• all_models
  • autobuild.htm (create_one_very_good_rebuilt_model_2)
  • autobuild.htm (create_20_very_good_rebuilt_models_that_are_as_different_as_possible_2)
• all_plausible_sg_list
  • automr.htm (all_plausible_sg_list)
  • automr.htm (use_all_plausible_sg)
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• all_sinusoidal
  • refinement.htm (dihedral_function_type)
  • pdbtools.htm (dihedral_function_type)
• allow_negative_f_double_prime
  • autosol.htm (allow_negative_f_double_prime)
• allow_negative_residues
  • autobuild.htm (allow_negative_residues)
• alpha_beta
  • refinement.htm (b23)
• alphanumeric
  • phenix_gui.htm (projects_2)
• alternate_nonbonded_off_on
  • pdbtools.htm (alternate_nonbonded_off_on)
• alternately
  • reflection_file_editor.htm (dealing_with_r-free_flags_2)
  • phaser_mr.htm (input_files_and_mandatory_parameters_2)
• ambiguity
  • hyss.htm (nsf_d2_peak_sca_2)
  • emma.htm (anch1)
• angle_ideal
  • refinement.htm (definition_of_custom_bonds_and_angles_2)
  • refinement.htm (angle_ideal)
• angles_rmsd_max
  • refinement.htm (angles_rmsd_max)
• angular_step
  • refinement.htm (angular_step)
• aniso_correct
  • refinement.htm (refinement_using_twinned_data_2)
  • refinement.htm (aniso_correct)
  • tutorial_twin.htm (map_inspection_2)
• anisob
  • tutorial_sad.htm (final_phasing_with_phaser_2)
• anisotropic_scaling
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • refinement.htm (anisotropic_scaling)
• anisotropy
  • faqs.htm
  • refinement.htm (refinement_using_twinned_data_2)
  • refinement.htm (relevant_reading_2)
  • autosol.htm (datafile_formats_in_autosol_4)
  • autosol.htm (analyzing_and_scaling_the_data_4)
• anisotropy_min
  • refinement.htm (anisotropy_min)
• anomalous
  • phenix-modules.htm (literature_2)
  • faqs.htm (can_phenix_do_mrsad__2)
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • faqs.htm (how_do_i_know_what_my_choices_of_labels_are_for_my_data_file__2)
  • refinement.htm
• anomalous_difference_map
  • refinement.htm (fill_missing_f_obs_with_weighted_f_model_3)
• anomalous_scatterers
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (selection)
• anoonly
  • autosol.htm (inano)
  • autosol.htm (inano_list)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_2)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_5)
• antiparallel
  • tutorial_mir.htm (how_do_i_know_if_i_have_a_good_solution__2)
  • tutorial_mad.htm (how_do_i_know_if_i_have_a_good_solution__2)
  • tutorial_sad.htm (how_do_i_know_if_i_have_a_good_solution__2)
• any_offset
  • get_cc_mtz_pdb.htm (any_offset)
  • get_cc_mtz_mtz.htm (any_offset)
• apply_back_trace_of_b_cart
  • refinement.htm (apply_back_trace_of_b_cart)
• apply_cif_link
  • refinement.htm (cif_modifications_and_links_2)
  • refinement.htm (residue_selection)
  • pdbtools.htm (residue_selection)
• apply_cif_modification
  • refinement.htm (cif_modifications_and_links_2)
  • refinement.htm (proceed_with_excessive_length_bonds)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__4)
  • pdbtools.htm (proceed_with_excessive_length_bonds)
• apply_operator
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (task_1)
  • xmanip.htm (b_iso)
• apply_sigma_scaling
  • refinement.htm (electron_density_maps_2)
  • refinement.htm (apply_sigma_scaling)
• apply_volume_scaling
  • refinement.htm (electron_density_maps_2)
  • refinement.htm (apply_volume_scaling)
• approximations
  • refinement.htm (fft_vs_direct)
• arbitary
  • create_maps.htm (the_"_create_maps"_gui_2)
• as_double
  • xmanip.htm (examples_2)
• assemble
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
  • find_helices_strands.htm (assemble)
• assessment
  • running-phenix.htm (command_line_interface_3)
  • xtriage.htm
  • xtriage.htm (literature_2)
  • phenix_gui.htm (reflection_tools_2)
  • tutorial_mir.htm (running_phenix_xtriage_2)
• assorted
  • phaser_mr.htm (additional_parameters_2)
• assumes
  • reflection_file_editor.htm (dealing_with_r-free_flags_2)
• asu_contents
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (expert_level)
• asuset
  • autosol.htm (specific_limitations_and_problems_7)
  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_9)
  • automr.htm (specific_limitations_and_problems_9)
  • running-wizards.htm (specific_limitations_and_problems__7)
• asymmetric
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • faqs.htm
  • refinement.htm (use_lattice_symmetry_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_13)
  • autosol.htm (specific_limitations_and_problems_3)
• atom_id
  • refinement.htm (cif_modifications_and_links_2)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__3)
• atom_radius
  • refinement.htm (atom_radius)
  • refinement.htm (number_of_grid_points)
• atom_selection
  • refinement.htm (electron_density_maps_2)
  • refinement.htm (atom_selection)
  • refinement.htm (atom_selection_1)
  • refinement.htm (atom_selection_2)
  • pdbtools.htm (atom_selection)
• atom_selection_buffer
  • refinement.htm (atom_selection_buffer)
• atom_type
  • autosol.htm (setting_up_inputs_7)
  • autosol.htm (how_to_run_the_autosol_wizard_5)
  • autosol.htm (how_to_run_the_autosol_wizard_6)
  • autosol.htm (mad_dataset_3)
  • autosol.htm (mad_dataset_selecting_particular_datasets_from_an_mtz_file_2)
• atomic
  • phenix-modules.htm (data_analysis_3)
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_scenarios_2)
• atomtype
  • tutorial_sad.htm (final_phasing_with_phaser_2)
• auto_mr
  • phaser.htm (general_strategy_for_automated_molecular_replacement_2)
  • phaser.htm (how_to_select_peaks_2)
• autobuild
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (command_line_interface_5)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
• autobuild_combine
  • tutorial_rebuild.htm
• autobuild_facts
  • autobuild.htm (output_files_from_autobuild_3)
• autobuild_input_labels
  • faqs.htm
• autobuild_lores
  • tutorial_rebuild.htm (what_parameters_did_i_use__2)
  • tutorial_build.htm (what_parameters_did_i_use__2)
• autobuild_summary
  • faqs.htm
  • autobuild.htm (output_files_from_autobuild_3)
  • tutorial_rebuild.htm
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file)
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
• autobuild_variables
  • automr.htm (specifying_a_refinement_file_for_autobuild_3)
  • automr.htm (semet)
• autobuild_warnings
  • autobuild.htm (output_files_from_autobuild_3)
• automates
  • phaser_ep.htm (anch1)
• automatic_randomization_if_all_equal
  • refinement.htm (automatic_randomization_if_all_equal)
• automr
  • running-phenix.htm (command_line_interface_5)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • faqs.htm
  • faqs.htm
• automr_auto_mr
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• automr_facts
  • automr.htm (output_files_from_automr_6)
• automr_hires
  • tutorial_mr.htm (what_parameters_did_i_use__2)
• automr_summary
  • automr.htm (output_files_from_automr_4)
  • tutorial_mr.htm
  • tutorial_mr.htm (the_automr_summary_dat_summary_file)
  • tutorial_mr.htm (the_automr_summary_dat_summary_file_2)
• automr_warnings
  • automr.htm (output_files_from_automr_5)
• autoopen
  • autobuild.htm (output_files_from_autobuild_3)
• autosol
  • running-phenix.htm (command_line_interface_5)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (structure_refinement_3)
  • faqs.htm
• autosol_facts
  • autosol.htm (output_files_from_autosol_7)
• autosol_guess_setup_for_scaling
  • tutorial_mir.htm (guessing_cell_contents_and_scattering_factors_2)
  • tutorial_mad.htm (guessing_cell_contents_2)
  • tutorial_sad.htm (guessing_cell_contents_2)
• autosol_hires
  • tutorial_sad.htm (what_parameters_did_i_use__2)
• autosol_lores
  • tutorial_mir.htm (what_parameters_did_i_use__2)
  • tutorial_mad.htm (what_parameters_did_i_use__2)
• autosol_summary
  • autosol.htm (output_files_from_autosol_5)
  • tutorial_mir.htm
  • tutorial_mir.htm (the_autosol_summary_dat_summary_file)
  • tutorial_mir.htm (the_autosol_summary_dat_summary_file_2)
  • tutorial_mad.htm
• autosol_warnings
  • autosol.htm (output_files_from_autosol_6)
• average_power
  • refinement.htm (average_power)
• b factor
  • refinement.htm
  • refinement.htm (water_picking_2)
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (b_iso_min)
• b_base
  • refinement.htm (b_base)
  • refinement.htm (b_base_1)
  • pdbtools.htm (b_base)
• b_cart
  • refinement.htm (developers_tools_2)
  • refinement.htm (b_cart)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (k_overall)
• b_either
  • refinement.htm (water_picking_2)
• b_factor_weight
  • refinement.htm (b_factor_weight)
  • refinement.htm (b_factor_weight_1)
• b_individual
  • refinement.htm
• b_iso
  • refinement.htm (water_picking_2)
  • refinement.htm (b_iso)
  • xtriage.htm (b_iso)
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (b_iso)
• b_iso_max
  • refinement.htm (water_picking_2)
  • refinement.htm (b_iso_max)
  • refinement.htm (b_iso_max_1)
• b_iso_min
  • refinement.htm (water_picking_2)
  • refinement.htm (b_iso_min)
• b_overall
  • autosol.htm (b_overall)
  • autosol.htm (correct_aniso)
  • autosol.htm (resolve_command_list)
  • autobuild.htm (resolve_command_list)
  • ligandfit.htm (resolve_command_list)
• b_sol
  • refinement.htm (reflection_output_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
  • refinement.htm (developers_tools_2)
  • refinement.htm (b_sol)
  • xmanip.htm (command_line_interface_2)
• b_sol_grid_search_max
  • refinement.htm (b_sol_grid_search_max)
• b_sol_grid_search_min
  • refinement.htm (b_sol_grid_search_min)
• b_sol_max
  • refinement.htm (b_sol_max)
• b_sol_min
  • refinement.htm (b_sol_min)
• b_sol_step
  • refinement.htm (b_sol_step)
• b_tls
  • refinement.htm
• b_value
  • xtriage.htm (xtriage_keywords_in_detail_2)
• background
  • faqs.htm (how_do_i_run_autobuild_on_a_cluster__2)
  • autosol.htm (background)
  • autosol.htm (run_command)
  • autobuild.htm
  • autobuild.htm (background)
• background_map
  • autobuild.htm (background_map)
• backslash
  • refinement.htm (atom_selection_examples_2)
  • tutorial_mr.htm (running_the_demo_a2u-globulin-mr_data_with_automr_2)
  • tutorial_rebuild.htm (running_the_demo_a2u-globulin-rebuild_data_with_autobuild_2)
  • tutorial_build.htm (running_the_demo_p9-build_data_with_autobuild_2)
  • tutorial_sad.htm (running_the_demo_p9_data_with_autosol_2)
• base_model
  • autobuild.htm (base_model)
• base_path
  • autosol.htm (base_path)
  • autobuild.htm (base_path)
  • ligandfit.htm (base_path)
  • automr.htm (base_path)
  • find_all_ligands.htm (base_path)
• basic_wilson
  • xtriage.htm (action_1)
• basis
  • what-is-phenix.htm (anch1_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_ligand_density_analysis_3)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • xtriage.htm (xtriage_keywords_in_detail_2)
• bayes
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (score_type_list)
  • autosol.htm (overall_score_method)
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• bayesian
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (scoring_of_heavy-atom_solutions_11)
  • autosol.htm (literature_3)
  • autosol.htm (overall_score_method)
• beamstop
  • refinement.htm (outliers_rejection_2)
  • xtriage.htm (action_1)
  • xtriage.htm (level_1)
• become_expert
  • elbow.htm (additional_programs_2)
• become_novice
  • elbow.htm (additional_programs_2)
• best_of_n_hyss
  • autosol.htm (good_cc_hyss)
  • autosol.htm (best_of_n_hyss)
  • autosol.htm (best_of_n_hyss_always)
  • autosol.htm (min_fraction_of_sites_found)
• best_of_n_hyss_always
  • autosol.htm (good_cc_hyss)
  • autosol.htm (best_of_n_hyss)
  • autosol.htm (best_of_n_hyss_always)
  • autosol.htm (min_fraction_of_sites_found)
• beta
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___2)
  • autosol.htm (unit_cell)
  • autobuild.htm (unit_cell)
  • ligandfit.htm (unit_cell)
  • automr.htm (automr_searching_for_2_components_3)
• bf_atoms_absent
  • refinement.htm (bf_atoms_absent)
• bfgs
  • refinement.htm (relevant_reading_2)
• bijvoet
  • refinement.htm (refining_with_anomalous_data_or_what_phenix_refine_does_with_fobs_and_fobs-__2)
  • autosol.htm (input_refinement_file)
  • autobuild.htm (refinement_file)
  • xtriage.htm (interpreting_xtriage_output_2)
  • reflection_statistics.htm (anch1)
• bond_angle_deviations_from_ideal
  • refinement.htm (bond_angle_deviations_from_ideal)
  • pdbtools.htm (bond_angle_deviations_from_ideal)
• bond_angle_restraints_sorted_by_residual
  • refinement.htm (bond_angle_restraints_sorted_by_residual)
  • pdbtools.htm (bond_angle_restraints_sorted_by_residual)
• bond_cutoff
  • ready_set.htm (bond_cutoff)
• bond_detection_distance_tolerance
  • refinement.htm (bond_detection_distance_tolerance)
  • pdbtools.htm (bond_detection_distance_tolerance)
• bond_lengths
  • refinement.htm (bond_lengths)
  • pdbtools.htm (bond_lengths)
• bond_max_distance
  • refinement.htm (bond_max_distance)
  • pdbtools.htm (bond_max_distance)
• bond_min_distance
  • refinement.htm (bond_min_distance)
  • pdbtools.htm (bond_min_distance)
• bond_restraints_sorted_by_residual
  • refinement.htm (bond_restraints_sorted_by_residual)
  • pdbtools.htm (bond_restraints_sorted_by_residual)
• bonding
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • refinement.htm (relevant_reading_2)
  • elbow.htm (novice_options__262)
  • reel.htm (input_3)
  • validation.htm (all-atom_contacts_2)
• bondlengths
  • ready_set.htm (use_default_bondlengths)
• bonds_rmsd_max
  • refinement.htm (bonds_rmsd_max)
• bootstrap
  • find_helices_strands.htm
  • find_helices_strands.htm (using_find_helices_strands_to_bootstrap_phenix_autobuild_)
  • find_helices_strands.htm (using_find_helices_strands_to_bootstrap_phenix_autobuild__2)
• boundary
  • autobuild.htm (offset_boundary)
  • autobuild.htm (boundary_background_map)
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__7)
  • multi_crystal_average.htm (use_model_mask)
  • multi_crystal_average.htm (write_ncs_domain_pdb)
• boundary_background_map
  • autobuild.htm (boundary_background_map)
  • autobuild.htm (offset_boundary_background_map)
• britton
  • phenix-modules.htm (data_analysis_3)
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_twin.htm (examples_2)
• bromide
  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
• buccaneer
  • autosol.htm (build_type)
  • autobuild.htm (build_type)
  • automr.htm (build_type)
• buffer
  • create_maps.htm (the_"_create_maps"_gui_2)
• build
  • faqs.htm (what_sample_data_are_available_to_run_automatically__2)
  • faqs.htm
  • faqs.htm
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___2)
  • refinement.htm (hydrogens_in_refinement_2)
• build_combine
  • tutorial_mad.htm (model-building_with_resolve_2)
• build_gui
  • automr.htm (build_gui)
• build_ias_types
  • refinement.htm (build_ias_types)
• build_model
  • autobuild.htm (build_outside)
  • autobuild.htm (connect)
  • autobuild.htm (insert_helices)
• build_only
  • refinement.htm (build_only)
• build_outside
  • autobuild.htm (build_outside)
  • tutorial_build.htm (model-building_with_resolve_2)
• build_outside_model
  • faqs.htm (how_can_i_specify_a_mask_for_density_modification_in_autosol_autobuild__2)
• build_scoring
  • autosol.htm (minimum_improvement)
• build_type
  • autosol.htm (build_type)
  • autosol.htm (n_cycle_build)
  • autobuild.htm (build_type)
  • automr.htm (build_type)
• builder
  • what-is-phenix.htm (anch1_3)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • elbow.htm
  • elbow.htm (anch1)
  • elbow.htm (purpose_4)
• bulk_and_scale_parameters
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (use_bulk_and_scale)
• bulk_solvent
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • refinement.htm (bulk_solvent)
• bulk_solvent_and_scale
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
  • refinement.htm (bulk_solvent_and_scale)
  • refinement.htm (bulk_solvent_and_scale_1)
  • refinement.htm (min_cubicle_edge_1)
• bunkóczi
  • what-is-phenix.htm (anch1_6)
  • faqs.htm (how_should_i_cite_phenix__2)
• c_rep
  • refinement.htm (trajectory_directory)
  • refinement.htm (c_rep)
• calc
  • refinement.htm (method)
  • create_maps.htm (the_"_create_maps"_gui_2)
  • create_maps.htm (guidelines_for_use_2)
• calc_factor
  • refinement.htm (electron_density_maps_2)
  • refinement.htm (calc_factor)
  • refinement.htm (calc_factor_1)
  • refinement.htm (calc_factor_2)
  • refinement.htm (calc_factor_3)
• calc_labels
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (calc_labels)
• carry_on
  • autosol.htm (carry_on)
  • autobuild.htm (carry_on)
  • ligandfit.htm (carry_on)
  • automr.htm (carry_on)
  • find_all_ligands.htm (carry_on)
• cartesian_dynamics
  • refinement.htm (rexp)
• cbetadev
  • phenix_gui.htm (validation_2)
• cc_denmod
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_8)
  • autosol.htm (score_type_list)
• cc_helix_min
  • autosol.htm (cc_helix_min)
  • autobuild.htm (cc_helix_min)
  • find_helices_strands.htm (cc_helix_min)
• cc_map_1_type
  • refinement.htm (cc_map_1_type)
• cc_map_2_type
  • refinement.htm (water_picking_2)
  • refinement.htm (cc_map_2_type)
• cc_min
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (number_of_ligands)
  • find_all_ligands.htm (cc_min)
• cc_obs
  • xtriage.htm (interpreting_xtriage_output_2)
• cc_perfect
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
• cc_rms
  • autosol.htm (score_type_list)
• cc_start
  • tutorial_ligandfit.htm (the_ligandfit_summary_dat_summary_file_2)
• cc_strand_min
  • autosol.htm (cc_strand_min)
  • autobuild.htm (cc_strand_min)
  • find_helices_strands.htm (cc_strand_min)
• cci_apps
  • hyss.htm (command_line_options_2)
• ccp4_mtz
  • find_ncs.htm (standard_run_of_find_ncs__4)
• ccp4_open
  • running-solve-resolve.htm (running_solve_resolve_from_the_command-line_or_in_a_script__4)
• ccp4_style_graphs
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (ccp4_style_graphs)
• cctbx
  • what-is-phenix.htm (anch1_4)
  • refinement.htm (relevant_reading_2)
  • autobuild.htm (automation_and_user_control_3)
  • xmanip.htm (parameters_and_definitions_2)
  • refine_gui.htm (acknowledgements_2)
• center_orth
  • simple_ncs_from_pdb.htm (standard_run_of_simple_ncs_from_pdb__6)
• centric
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage.htm (specific_limitations_and_problems_2)
  • reflection_statistics.htm (anch1)
  • tutorial_mir.htm (final_phasing_with_solve_2)
  • tutorial_sad.htm (final_phasing_with_phaser_2)
• centring_type
  • explore_metric_symmetry.htm (keywords_2)
  • explore_metric_symmetry.htm (examples_2)
• chain_id
  • fit_loops.htm (standard_run_of_fit_loops__2)
  • fit_loops.htm (chain_id)
  • fit_loops.htm (start)
  • fit_loops.htm (end)
• chain_id_increment
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (chain_id_increment)
• chain_type
  • autosol.htm (sad_dataset_building_rna_instead_of_protein_2)
  • autosol.htm (chain_type)
  • autobuild.htm (including_ligand_coordinates_in_autobuild_3)
  • autobuild.htm (build_an_rna_chain_2)
  • autobuild.htm (build_a_dna_chain_2)
• change_sg
  • autosol.htm (change_sg)
• change_to_space_group
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• check_residues_against_monomer_lib
  • elbow.htm (additional_programs_2)
• chir_volume_esd
  • refinement.htm (chir_volume_esd)
  • pdbtools.htm (chir_volume_esd)
• chiral
  • autosol.htm (running_autosol_separately_in_related_space_groups__2)
  • elbow.htm (novice_options__178)
  • elbow.htm (novice_options__182)
  • elbow.htm (novice_options__184)
  • reel.htm (editing_4)
• chiral_volume_deviations_from_ideal
  • refinement.htm (chiral_volume_deviations_from_ideal)
  • pdbtools.htm (chiral_volume_deviations_from_ideal)
• chiralities
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (chiralities)
  • pdbtools.htm (anch1)
• chirality
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (cif_modifications_and_links_2)
  • elbow.htm (novice_options__188)
  • validation.htm (validation_of_protein_geometry_2)
• chirality_restraints_sorted_by_residual
  • refinement.htm (chirality_restraints_sorted_by_residual)
  • pdbtools.htm (chirality_restraints_sorted_by_residual)
• cif
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • refinement.htm
  • refinement.htm (phenix_refine_organization_2)
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
• cif_def_file_list
  • autosol.htm (cif_def_file_list)
  • autobuild.htm (including_ligand_coordinates_in_autobuild_7)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__3)
  • autobuild.htm (cif_def_file_list)
  • ligandfit.htm (cif_def_file_list)
• cif_def_files_list
  • autobuild.htm (input_lig_file_list)
• cif_dir_name
  • ready_set.htm (cif_dir_name)
• cif_file_name
  • ready_set.htm (cif_file_name)
• cif_link
  • refinement.htm (cif_modifications_and_links_2)
• cif_modification
  • refinement.htm (cif_modifications_and_links_2)
• cis_threshold
  • refinement.htm (cis_threshold)
  • pdbtools.htm (cis_threshold)
• cispep
  • refinement.htm (cif_modifications_and_links_2)
• clash_guard
  • refinement.htm (residues_with_excluded_nonbonded_symmetry_interactions)
  • pdbtools.htm (residues_with_excluded_nonbonded_symmetry_interactions)
• clashlist
  • molprobity_tool.htm (authors_2)
• clashscore
  • autobuild.htm (include_molprobity)
  • autobuild.htm (ok_molp_score)
  • autobuild.htm (scale_molp_score)
  • phenix_gui.htm (validation_2)
  • validation.htm (overview_2)
• clean_up
  • autosol.htm (clean_up)
  • autobuild.htm (clean_up)
  • ligandfit.htm (clean_up)
  • automr.htm (clean_up)
  • find_all_ligands.htm (clean_up)
• cluster
  • faqs.htm (how_do_i_run_autobuild_on_a_cluster__2)
  • autosol.htm (max_wait_time)
  • autosol.htm (run_command)
  • autobuild.htm
  • autobuild.htm (max_wait_time)
• clusters
  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
• cmtz
  • reflection_file_tools.htm (phenix_mtz_dump_2)
• cns_as_mtz
  • reflection_file_tools.htm
  • reflection_file_tools.htm (phenix_cns_as_mtz)
  • reflection_file_tools.htm (phenix_cns_as_mtz_2)
• cns_file
  • reflection_file_tools.htm (phenix_cns_as_mtz_2)
• cns_solve
  • hyss.htm (mbp_hkl_2)
• coarse_grid
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
  • faqs.htm (what_do_i_do_if_autobuild_says_tried_resolve_extra_huge__but_not_ok__2)
  • autosol.htm (resolve_command_list)
  • autobuild.htm (resolve_command_list)
  • ligandfit.htm (resolve_command_list)
• combine_extend
  • autobuild.htm (use_cc_in_combine_extend)
  • tutorial_mir.htm (model-building_with_resolve_2)
  • tutorial_mad.htm (model-building_with_resolve_2)
• combine_map
  • faqs.htm
• combine_only
  • autobuild.htm (combine_only)
• combine_siblings
  • autosol.htm (combine_siblings)
• command_line
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • autosol.htm (data)
  • autosol.htm (solve_command_list)
  • autobuild.htm (find_ncs)
  • ligandfit.htm
• comments_in_params_file
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
• compare_file
  • find_helices_strands.htm (compare_file)
• compare_two_molecules
  • elbow.htm (additional_programs_2)
• completeness_cut
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (completeness_cut)
• complex_fcalc
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (output)
• component
  • refinement.htm
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • automr.htm (components_copies_search_models_and_ensembles_4)
  • automr.htm (components_copies_search_models_and_ensembles_5)
  • automr.htm (running_from_a_parameters_file_3)
• component_copies
  • faqs.htm
  • automr.htm (running_from_a_parameters_file_3)
  • automr.htm (automr_searching_for_2_components_3)
  • automr.htm (specifying_molecular_masses_of_2_components_3)
  • automr.htm
• component_type
  • automr.htm (running_from_a_parameters_file_3)
  • automr.htm (automr_searching_for_2_components_3)
  • automr.htm (specifying_molecular_masses_of_2_components_3)
  • automr.htm
  • automr.htm (component_type)
• composite_omit
  • autobuild.htm (omit_region_specification)
• composite_omit_type
  • faqs.htm
  • autobuild.htm (make_a_sa-omit_map_around_atoms_in_target_pdb_2)
  • autobuild.htm (make_a_simple_composite_omit_map_2)
  • autobuild.htm (make_a_sa_composite_omit_map_2)
  • autobuild.htm (make_an_iterative-build_omit_map_around_atoms_in_target_pdb_2)
• composition
  • faqs.htm
  • automr.htm (summary_of_inputs_and_outputs_for_automr_4)
  • automr.htm (weight_seq_list)
  • xtriage.htm (interpreting_xtriage_output_2)
  • phaser.htm
• composition_num_list
  • automr.htm (composition_num_list)
• compounds
  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
• compute_optimal_errors
  • refinement.htm (compute_optimal_errors)
• concatenate_model
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (concatenate_model)
• conformer
  • refinement.htm (occupancy_refinement_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
• consider_main_chain_list
  • faqs.htm
  • autobuild.htm (base_model)
  • autobuild.htm (consider_main_chain_list)
  • autobuild.htm (model_list)
  • find_helices_strands.htm (using_find_helices_strands_to_bootstrap_phenix_autobuild__2)
• consideration
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_extra_unique_solutions)
  • ligandfit.htm (existing_ligand_file_list)
  • find_all_ligands.htm (existing_ligand_file_list)
• constrain_dihedrals_with_sigma_less_than
  • refinement.htm (constrain_dihedrals_with_sigma_less_than)
• constrained
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_scenarios_2)
  • refinement.htm (occupancy_refinement_2)
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
• constrained_group
  • refinement.htm (occupancy_refinement_2)
  • refinement.htm (remove_selection)
• contact_dist
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (use_contact_order)
  • map_to_object.htm (contact_dist)
• continue_autosol
  • running-wizards.htm (keeping_track_of_multiple_runs_of_a_wizard_from_the_gui__5)
• contribute
  • phaser_mr.htm (input_files_and_mandatory_parameters_2)
• contribute_to_f_calc
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (contribute_to_f_calc)
• convergence_test
  • refinement.htm (convergence_test)
  • refinement.htm (convergence_test_1)
• convert_to_anisotropic
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_2)
  • refinement.htm (convert_to_anisotropic)
  • pdbtools.htm (convert_to_anisotropic)
• convert_to_isotropic
  • refinement.htm
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_2)
  • refinement.htm (convert_to_isotropic)
  • pdbtools.htm (convert_to_isotropic)
• convolution
  • find_helices_strands.htm (how_find_helices_strands_finds_rna_and_dna_helices_in_maps__2)
  • find_helices_strands.htm (res_convolution)
• cool_rate
  • refinement.htm (cool_rate)
• coordinate_sigma
  • refinement.htm (coordinate_sigma)
  • refinement.htm (coordinate_sigma_1)
  • autobuild.htm (specifying_phenix_refine_parameters_16)
• coordination
  • elbow.htm (additional_programs_2)
  • ready_set.htm
  • ready_set.htm (purpose_2)
  • ready_set.htm (metal_coordination)
  • ready_set.htm (metals)
• coot_name
  • autosol.htm (coot_name)
  • autobuild.htm (coot_name)
• copies_to_find
  • automr.htm (running_from_a_parameters_file_3)
  • automr.htm (automr_searching_for_2_components_3)
  • automr.htm (specifying_molecular_masses_of_2_components_3)
  • automr.htm
  • automr.htm (copies)
• copy_run
  • autosol.htm (copy_run)
  • autobuild.htm (copy_run)
  • ligandfit.htm (copy_run)
  • automr.htm (copy_run)
  • find_all_ligands.htm (copy_run)
• corr_rms
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_7)
  • autosol.htm (score_type_list)
  • autosol.htm (overall_score_method)
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• correct_aniso
  • autosol.htm (analyzing_and_scaling_the_data_5)
  • autosol.htm (input_refinement_file)
  • autosol.htm (b_overall)
  • autosol.htm (correct_aniso)
  • autosol.htm (delta_b_for_auto_correct_aniso)
• correct_drifted_waters
  • refinement.htm (correct_drifted_waters)
• cos_sin_table
  • refinement.htm (cos_sin_table)
  • refinement.htm (cos_sin_table_1)
  • pdbtools.htm (cos_sin_table)
• coval
  • refinement.htm (cif_modifications_and_links_2)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__3)
• create_maps
  • create_maps.htm (anch1)
  • create_maps.htm (guidelines_for_use_2)
• create_scoring_table
  • autosol.htm (create_scoring_table)
• crossover
  • autobuild.htm (dist_close)
• crystal_info
  • autosol.htm (labels)
  • autobuild.htm (hires_file)
  • ligandfit.htm (quick)
  • automr.htm (component_copies)
  • find_all_ligands.htm (quick)
• crystal_symmetry
  • refinement.htm (list_of_all_refinement_keywords_2)
  • refinement.htm (poor_map_value_threshold)
  • superpose_pdbs.htm (pdb_file_name_moving)
  • pdbtools.htm (file_name_2)
• cshrc
  • phenix-environment.htm (setting_up_your_environment_2)
  • tutorial_mir.htm (setting_up_to_run_phenix_2)
  • tutorial_mr.htm (setting_up_to_run_phenix_2)
  • tutorial_ligandfit.htm (setting_up_to_run_phenix_2)
  • tutorial_rebuild.htm (setting_up_to_run_phenix_2)
• current_cycle
  • autosol.htm (output_files_from_autosol_13)
• current_cycle_eval
  • autosol.htm (output_files_from_autosol_13)
• current_cycle_map_coeffs
  • autosol.htm (output_files_from_autosol_10)
• current_model
  • tutorial_rebuild.htm
• custom_par_1
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
• customization
  • old_gui.htm (strategies_4)
• cutoff_trace
  • find_helices_strands.htm (cutoff_trace)
• d66
  • what-is-phenix.htm (anch1_6)
  • faqs.htm (how_should_i_cite_phenix__2)
  • validation.htm (references_2)
• d_max
  • xtriage.htm (interpreting_xtriage_output_2)
  • hyss.htm (command_line_options_2)
  • reflection_statistics.htm (anch1)
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• d_max_textal
  • autosol.htm (d_max_textal)
• d_min
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage.htm (d_min)
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (d_min)
  • hyss.htm (command_line_options_2)
• d_min_textal
  • autosol.htm (d_min_textal)
• d_ncs
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (interpreting_xtriage_output_2)
• d_spacing
  • xtriage.htm (interpreting_xtriage_output_2)
• dano
  • autosol.htm (sad_dataset_selecting_a_particular_dataset_from_an_mtz_file_2)
  • autosol.htm (group_labels_list)
  • create_maps.htm (guidelines_for_use_2)
• data_anom
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (refining_with_anomalous_data_or_what_phenix_refine_does_with_fobs_and_fobs-__2)
  • refinement.htm (rejecting_reflections_by_sigma_2)
• data_label
  • hyss.htm (command_line_options_2)
• data_link
  • refinement.htm (cif_modifications_and_links_2)
  • refinement.htm (data_link)
  • pdbtools.htm (data_link)
• data_mod
  • refinement.htm (cif_modifications_and_links_2)
  • refinement.htm (data_mod)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__4)
  • pdbtools.htm (data_mod)
• data_neutron
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_2)
• data_quality
  • autosol.htm (data_quality)
• data_xray
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_2)
• database
  • faqs.htm
  • faqs.htm
  • faqs.htm
  • running-solve-resolve.htm (running_solve_resolve_from_the_command-line_or_in_a_script__6)
  • elbow.htm
• databases
  • running-wizards.htm (specific_limitations_and_problems__6)
  • molprobity_tool.htm (authors_2)
• datafile
  • autosol.htm
  • autosol.htm (setting_up_inputs_4)
  • autosol.htm (datafile_formats_in_autosol)
  • autosol.htm (resolution_limits_in_autosol_9)
  • autosol.htm (how_to_run_the_autosol_wizard_4)
• datafile_labin_list
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__2)
  • multi_crystal_average.htm (datafile_labin_list)
• datafile_list
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__2)
  • multi_crystal_average.htm (datafile_list)
• dataman
  • reflection_file_editor.htm (dealing_with_r-free_flags_2)
• dataset
  • faqs.htm (are_any_of_the_sample_datasets_annotated__2)
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • faqs.htm (why_do_i_get_"_none_of_the_solve_versions_worked"_in_autosol__2)
  • autosol.htm
• datfiles
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__4)
• dayhoff
  • superpose_pdbs.htm (similarity_matrix)
• decision_making
  • autosol.htm (ignore_2)
  • autobuild.htm (refine_eff_file_list)
  • automr.htm (added_component)
• default_vdw_distance
  • refinement.htm (default_vdw_distance)
  • pdbtools.htm (default_vdw_distance)
• delete_runs
  • autosol.htm (delete_runs)
  • autobuild.htm (delete_runs)
  • ligandfit.htm (delete_runs)
  • automr.htm (delete_runs)
  • find_all_ligands.htm (delete_runs)
• delete_tmp_dir
  • find_helices_strands.htm (delete_tmp_dir)
• delta_b
  • autosol.htm (delta_b_for_auto_correct_aniso)
  • autosol.htm (ratio_b_for_auto_correct_aniso)
  • get_cc_mtz_pdb.htm (scale)
• delta_b_for_auto_correct_aniso
  • autosol.htm (analyzing_and_scaling_the_data_5)
  • autosol.htm (correct_aniso)
  • autosol.htm (delta_b_for_auto_correct_aniso)
  • autosol.htm (ratio_b_for_auto_correct_aniso)
• delta_phi_ligand
  • ligandfit.htm (delta_phi_ligand)
  • find_all_ligands.htm (delta_phi_ligand)
• delta_range_2p_max
  • refinement.htm (delta_range_2p_max)
  • pdbtools.htm (delta_range_2p_max)
• delta_range_2p_min
  • refinement.htm (delta_range_2p_min)
  • pdbtools.htm (delta_range_2p_min)
• delta_slack
  • refinement.htm (definition_of_custom_bonds_and_angles_2)
• density modification
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (tasks_and_strategies_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_model_building_3)
  • faqs.htm
• density_modification
  • autosol.htm (nat_der_list)
  • autobuild.htm (scale_molp_score)
• deprecated
  • phenix_gui.htm (overview_2)
• deriv_hyss_consensus_model
  • autosol.htm (sad_dataset_reading_heavy-atom_sites_from_a_pdb_file_written_by_phenix_hyss_2)
• descriptor
  • refinement.htm (list_of_all_refinement_keywords_2)
  • autosol.htm (list_of_all_autosol_keywords_2)
  • autobuild.htm (list_of_all_autobuild_keywords_2)
  • ligandfit.htm (list_of_all_ligandfit_keywords_2)
  • automr.htm (list_of_all_automr_keywords_2)
• desired_coverage
  • autosol.htm (desired_coverage)
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_extra_unique_solutions)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (what_to_do_next_2)
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  • refinement.htm (dihedral_function_type)
  • pdbtools.htm (dihedral_function_type)
• detwin
  • refinement.htm (refinement_using_twinned_data_2)
  • refinement.htm (twin_target)
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (action_2)
  • tutorial_twin.htm (map_inspection_2)
• dev_scoring
  • autosol.htm (trace_chain_score)
• dfmodel
  • refinement.htm (water_picking_2)
  • refinement.htm (map_type)
  • refinement.htm (fill_mode)
  • refinement.htm (primary_map_type)
  • refinement.htm (cc_map_2_type)
• dialogs
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• dictens
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• diff_map
  • refinement.htm (mode_6)
  • refinement.htm (model_map_name)
  • refinement.htm (real_space_target_weight)
  • refinement.htm (restraints_target_weight)
• diffraction_index_equivalent
  • emma.htm (anch1)
• dihedral_angle_deviations_from_ideal
  • refinement.htm (dihedral_angle_deviations_from_ideal)
  • pdbtools.htm (dihedral_angle_deviations_from_ideal)
• dihedral_angle_restraints_sorted_by_residual
  • refinement.htm (dihedral_angle_restraints_sorted_by_residual)
  • pdbtools.htm (dihedral_angle_restraints_sorted_by_residual)
• dihedral_function_type
  • refinement.htm (dihedral_function_type)
  • pdbtools.htm (dihedral_function_type)
• dihedrals
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (dihedrals)
  • elbow.htm (expert_options__88)
  • elbow.htm (expert_options__92)
  • reel.htm (editing_2)
• dimensions
  • reflection_file_editor.htm (notes_on_usage_2)
  • tutorial_mir.htm (running_phenix_xtriage_2)
  • tutorial_mr.htm (running_the_demo_a2u-globulin-mr_data_with_automr_2)
• direct methods
  • hyss.htm (hyss_overview_2)
  • hyss.htm (command_line_options_2)
  • tutorial_mir.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_mad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_sad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
• disable_suitability_test
  • refinement.htm (disable_suitability_test)
  • refinement.htm (disable_suitability_test_1)
• discard_psi_phi
  • refinement.htm (discard_psi_phi)
  • pdbtools.htm (discard_psi_phi)
• dispersive
  • refinement.htm (f_and_f_refinement_2)
  • tutorial_mad.htm (scaling_mad_data_and_estimating_fa_values_2)
• displacement
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm
  • refinement.htm (available_features_2)
  • refinement.htm
  • refinement.htm (relevant_reading_2)
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  • autosol.htm (display_all)
  • autobuild.htm (display_all)
  • ligandfit.htm (display_all)
  • automr.htm (display_all)
  • find_all_ligands.htm (display_all)
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  • autosol.htm (display_facts)
  • autobuild.htm (display_facts)
  • ligandfit.htm (display_facts)
  • automr.htm (display_facts)
  • find_all_ligands.htm (display_facts)
• display_labels
  • autosol.htm (sad_dataset_selecting_a_particular_dataset_from_an_mtz_file_3)
  • autosol.htm (mad_dataset_selecting_particular_datasets_from_an_mtz_file_3)
  • autosol.htm (labels)
  • autosol.htm (labels_1)
  • autosol.htm (labels_2)
• display_runs
  • autosol.htm (display_runs)
  • autobuild.htm (display_runs)
  • ligandfit.htm (display_runs)
  • automr.htm (display_runs)
  • find_all_ligands.htm (display_runs)
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  • autosol.htm (display_summary)
  • autobuild.htm (display_summary)
  • ligandfit.htm (display_summary)
  • automr.htm (display_summary)
  • find_all_ligands.htm (display_summary)
• dist_ca_start
  • find_helices_strands.htm (dist_ca_start)
• dist_ca_tol
  • find_helices_strands.htm (dist_ca_tol)
  • find_helices_strands.htm (target_p_ratio)
• dist_ca_tol_max
  • find_helices_strands.htm (dist_ca_tol_max)
• dist_close
  • autobuild.htm (dist_close)
  • autobuild.htm (rebuild_in_place)
• dist_close_overlap
  • autobuild.htm (keep_pdb_atoms)
  • autobuild.htm (dist_close_overlap)
• dist_connect_max_helices
  • autobuild.htm (dist_connect_max_helices)
• distance_ideal
  • refinement.htm (definition_of_custom_bonds_and_angles_2)
  • refinement.htm (distance_ideal)
• distance_model
  • refinement.htm (definition_of_custom_bonds_and_angles_2)
• distance_power
  • refinement.htm (distance_power)
• distortions
  • validation.htm (geometry_restraints_outliers_2)
• distributions
  • faqs.htm
  • faqs.htm
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_mir.htm (statistical_density_modification_with_resolve_2)
  • tutorial_mad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• disulfide_distance_cutoff
  • refinement.htm (disulfide_distance_cutoff)
  • pdbtools.htm (disulfide_distance_cutoff)
• dmin
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • autobuild.htm (specifying_other_general_parameters_3)
  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
  • tutorial_mir.htm (final_phasing_with_solve_2)
  • tutorial_mad.htm (choosing_datafiles_with_high_signal-to-noise_2)
• dna
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (cif_modifications_and_links_2)
  • refinement.htm (atom_selection_examples_2)
  • autosol.htm (sad_dataset_building_rna_instead_of_protein_2)
  • autosol.htm (chain_type)
• do_anisotropy_correction
  • automr.htm (do_anisotropy_correction)
• do_madbst
  • autosol.htm (do_madbst)
• documentation
  • what-is-phenix.htm
  • install.htm
  • phenix-environment.htm
  • phenix-environment.htm (documentation)
  • phenix-environment.htm (documentation_2)
• domain
  • phenix-modules.htm (automated_ligand_density_analysis_3)
  • refinement.htm (min_fraction_domain)
  • simple_ncs_from_pdb.htm (how_simple_ncs_from_pdb_works__7)
  • simple_ncs_from_pdb.htm (specific_limitations_and_problems__5)
  • simple_ncs_from_pdb.htm (min_fraction_domain)
• domain_finding_parameters
  • refinement.htm (dry_run)
  • simple_ncs_from_pdb.htm (dry_run)
  • multi_crystal_average.htm (dry_run_1)
• double_prime
  • autosol.htm (f_double_prime_1)
  • autosol.htm (f_double_prime_2)
  • autosol.htm (mad_ha_add_f_double_prime_list)
• dry_run
  • refinement.htm (running_phenix_refine_2)
  • refinement.htm (dry_run)
  • autosol.htm (dry_run)
  • autobuild.htm (dry_run)
  • ligandfit.htm (dry_run)
• echols
  • what-is-phenix.htm (anch1_6)
  • faqs.htm (how_should_i_cite_phenix__2)
• edit_chains
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__3)
  • multi_crystal_average.htm (run_of_phenix_multi_crystal_average_with_multiple_domains__4)
  • multi_crystal_average.htm (run_of_phenix_multi_crystal_average_with_multiple_domains__5)
• edit_model
  • tutorial_rebuild.htm (individual_rebuild-in-place_log_files__2)
• edit_pdb
  • autobuild.htm (create_one_very_good_rebuilt_model_2)
  • autobuild.htm (edit_pdb)
• edited_file
  • multi_crystal_average.htm (run_of_phenix_multi_crystal_average_with_multiple_domains__5)
• edited_pdb
  • autobuild.htm (general_limitations_2)
  • tutorial_rebuild.htm (deciding_on_rebuild-in-place_and_editing_input_pdb_file_2)
• eigen_mean
  • xtriage.htm (final_b)
• eigen_min
  • xtriage.htm (final_b)
• elbow_defaults
  • tutorial_elbow.htm (generating_ligand_restraints_using_pdb_file_2)
• elbow_tutorial
  • tutorial_elbow.htm (setup_2)
• electron density
  • what-is-phenix.htm (anch1_3)
  • running-phenix.htm (tasks_and_strategies_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_ligand_density_analysis_3)
  • refinement.htm
• electron_density_maps
  • refinement.htm (electron_density_maps_2)
  • refinement.htm (pickle_fmodel)
• element_symbol
  • hyss.htm (command_line_options_2)
• emma
  • hyss.htm
  • hyss.htm (phenix_emma)
  • hyss.htm (phenix_emma_2)
  • emma.htm (anch1)
• emulate_cartesian
  • refinement.htm (emulate_cartesian)
• enantiomer
  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
• enantiomorphic
  • autosol.htm (finding_heavy-atom_anomalously-scattering_atom_sites_3)
• endmdl
  • superpose_pdbs.htm (specific_limitations_and_problems__2)
  • phaser.htm (building_an_ensemble_from_coordinates_2)
• energy
  • refinement.htm (trajectory_directory)
  • autosol.htm (wavelength_name_1)
  • elbow.htm (novice_options__154)
  • tutorial_mad.htm (choosing_datafiles_with_high_signal-to-noise_2)
  • tutorial_elbow.htm (when_do_we_need_restraints_for_a_ligand__2)
• ense
  • phaser.htm (has_phaser_solved_it__2)
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• ensemble
  • refinement.htm (random_seed_2)
  • autobuild.htm (create_20_very_good_rebuilt_models_that_are_as_different_as_possible_2)
  • automr.htm (summary_of_inputs_and_outputs_for_automr_6)
  • automr.htm (summary_of_inputs_and_outputs_for_automr_7)
  • automr.htm (summary_of_inputs_and_outputs_for_automr_8)
• ensembleid
  • automr.htm (running_from_a_parameters_file_3)
  • automr.htm (automr_searching_for_2_components_3)
  • automr.htm (specifying_molecular_masses_of_2_components_3)
  • automr.htm
  • automr.htm (ensembleid)
• ensembler
  • phenix_gui.htm (model_tools_2)
• environment
  • what-is-phenix.htm (anch1_4)
  • phenix-environment.htm
  • phenix-environment.htm (setting_up_your_environment)
  • phenix-environment.htm (setting_up_your_environment_2)
  • running-phenix.htm (tasks_and_strategies_3)
• environmental
  • phenix-environment.htm (setting_up_your_environment_2)
  • running-solve-resolve.htm (running_solve_resolve_from_the_command-line_or_in_a_script__4)
• eps
  • refinement.htm (eps)
  • xmanip.htm (examples_2)
• epsilon_range_not_2p_max
  • refinement.htm (epsilon_range_not_2p_max)
  • pdbtools.htm (epsilon_range_not_2p_max)
• epsilon_range_not_2p_min
  • refinement.htm (epsilon_range_not_2p_min)
  • pdbtools.htm (epsilon_range_not_2p_min)
• equal_ncs_weight
  • multi_crystal_average.htm (equal_ncs_weight)
• errors
  • faqs.htm (why_does_autobuild_bomb_and_say_it_cannot_find_a_temp_file__2)
  • faqs.htm (why_does_the_autobuild_wizard_just_stop_after_a_few_seconds__2)
  • refinement.htm (relevant_reading_2)
  • autosol.htm (datafile_formats_in_autosol_4)
  • autobuild.htm (specific_limitations_and_problems_2)
• estimation_algorithm
  • refinement.htm (estimation_algorithm)
• euclidean
  • hyss.htm (phenix_emma_2)
  • emma.htm (anch1)
• euler
  • refinement.htm (euler_angle_convention)
  • refinement.htm (euler_angle_convention_1)
  • automr.htm (fixed_euler_list)
  • phaser.htm (has_phaser_solved_it__2)
  • pdbtools.htm (euler_angle_convention)
• euler_angle_convention
  • refinement.htm (euler_angle_convention)
  • refinement.htm (euler_angle_convention_1)
  • pdbtools.htm (euler_angle_convention)
• evaluate_model
  • faqs.htm (how_can_i_specify_a_mask_for_density_modification_in_autosol_autobuild__2)
• evenly
  • reflection_file_editor.htm (dealing_with_r-free_flags_2)
• every_macro_cycle
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (water_picking_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (mode)
  • refinement.htm (mode_1)
• example_name
  • faqs.htm (what_sample_data_are_available_to_run_automatically__2)
  • examples.htm (what_sample_data_are_available_to_run_automatically__2)
• excessive_bond_distance_limit
  • refinement.htm (excessive_bond_distance_limit)
• excessive_distance_limit
  • refinement.htm (excessive_distance_limit)
• excessive_temperature_factor
  • refinement.htm (excessive_temperature_factor)
• existing_ligand_file_list
  • ligandfit.htm (existing_ligand_file_list)
  • find_all_ligands.htm (existing_ligand_file_list)
• exp_table_one_over_step_size
  • refinement.htm (exp_table_one_over_step_size)
  • refinement.htm (exp_table_one_over_step_size_1)
  • pdbtools.htm (exp_table_one_over_step_size)
• experimental_phases
  • refinement.htm (use_lattice_symmetry_1)
• expert_level
  • xtriage.htm (expert_level)
• explore_metric_symmetry
  • xtriage.htm (interpreting_xtriage_output_2)
  • explore_metric_symmetry.htm (purpose_2)
  • explore_metric_symmetry.htm (keywords_2)
  • explore_metric_symmetry.htm (examples_2)
• export_final_f_model
  • refinement.htm (reflection_output_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
  • refinement.htm (export_final_f_model)
• exposes
  • phenix_gui.htm (phasing_2)
  • phaser_mr.htm (anch1)
• expt_type
  • autosol.htm (expt_type)
• exptl_fobs_freer_flags
  • autobuild.htm (and_optional_files_2)
• exptl_fobs_phases_freer_flags
  • faqs.htm
  • autobuild.htm (output_files_from_autobuild_3)
  • tutorial_rebuild.htm (generation_of_freer_flags_2)
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_build.htm (generation_of_freer_flags_2)
• ext_ref_files
  • faqs.htm
• extend_only
  • autobuild.htm (rebuild_side_chains)
• extend_try_list
  • autobuild.htm (extend_try_list)
  • ligandfit.htm (extend_try_list)
  • find_all_ligands.htm (extend_try_list)
• extensive_build
  • autobuild.htm (extensive_build)
• extra_cells_to_search
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (extra_cells_to_search)
• extra_thorough
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
• extra_thorough_randomize
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
• extra_verbose
  • autosol.htm (extra_verbose)
  • autobuild.htm (extra_verbose)
  • ligandfit.htm (extra_verbose)
  • automr.htm (extra_verbose)
  • find_all_ligands.htm (extra_verbose)
• extreme_wilson
  • xtriage.htm (level)
• f_as_f_sq
  • xmanip.htm (examples_2)
• f_double_prime
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (f_double_prime)
  • refinement.htm (refine)
  • autosol.htm (setting_up_inputs_8)
  • autosol.htm (how_to_run_the_autosol_wizard_3)
• f_double_prime_list
  • autosol.htm (f_double_prime_list)
• f_mean
  • refinement.htm (refining_with_anomalous_data_or_what_phenix_refine_does_with_fobs_and_fobs-__2)
• f_model
  • pdbtools.htm (anch1)
  • pdbtools.htm (action)
  • pdbtools.htm (space_group)
• f_prime
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (f_prime)
  • refinement.htm (refine)
  • autosol.htm (setting_up_inputs_8)
  • autosol.htm (how_to_run_the_autosol_wizard_3)
• f_prime_list
  • autosol.htm (f_prime_list)
• fake
  • phenix_gui.htm (model_tools_2)
• fake_f_obs
  • refinement.htm (developers_tools_2)
  • refinement.htm (fake_f_obs)
  • refinement.htm (file_name_7)
• falling
  • phaser_ep.htm (anch1)
• fc_difference_map
  • ligandfit.htm (sample_command_line_inputs_3)
  • ligandfit.htm (lig_map_type)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (lig_map_type)
  • tutorial_ligandfit.htm (what_to_do_next_2)
• fcalc
  • refinement.htm (reflection_output_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
  • refinement.htm (developers_tools_2)
  • refinement.htm (fft_vs_direct)
  • refinement.htm (contribute_to_f_calc)
• fft_vs_direct
  • refinement.htm (fft_vs_direct)
• file_info
  • ligandfit.htm (space_group)
  • find_all_ligands.htm (space_group)
• file_name
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_2)
  • refinement.htm (file_name)
  • refinement.htm (file_name_1)
  • refinement.htm (file_name_2)
  • refinement.htm (file_name_3)
• file_or_file_list
  • ligandfit.htm (sample_command_line_inputs_8)
  • ligandfit.htm (file_or_file_list)
  • find_all_ligands.htm (file_or_file_list)
• file_prefix
  • refinement.htm (file_prefix)
• file_with_list_of_files
  • ligandfit.htm (sample_command_line_inputs_8)
  • ligandfit.htm (file_or_file_list)
  • find_all_ligands.htm (file_or_file_list)
• fill_gaps
  • find_helices_strands.htm (fill_gaps)
• fill_missing_f_obs_with_weighted_f_model
  • refinement.htm (fill_missing_f_obs_with_weighted_f_model)
  • refinement.htm (fill_missing_f_obs_with_weighted_f_model_1)
  • refinement.htm (fill_missing_f_obs_with_weighted_f_model_2)
  • refinement.htm (fill_missing_f_obs_with_weighted_f_model_3)
• fill_mode
  • refinement.htm (fill_mode)
• filled_2fofc_maps
  • autobuild.htm (filled_2fofc_maps)
• filter_at_start
  • refinement.htm (filter_at_start)
• filter_only
  • refinement.htm (water_picking_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (mode_1)
• final_b
  • xtriage.htm (final_b)
• final_error
  • refinement.htm (final_error)
• final_geometry
  • elbow.htm (geometry_optimisation_2)
• final_temperature
  • refinement.htm (final_temperature)
• final_temperature_kelvin
  • refinement.htm (final_temperature_kelvin)
• find_all_ligands
  • find_all_ligands.htm
  • find_all_ligands.htm (author_s__2)
  • find_all_ligands.htm (purpose_2)
  • find_all_ligands.htm (how_phenix_find_all_ligands_works_)
  • find_all_ligands.htm (how_phenix_find_all_ligands_works__2)
• find_and_add_hydrogens
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (find_and_add_hydrogens)
• find_automatically
  • refinement.htm (using_ncs_restraints_in_refinement_2)
  • refinement.htm (find_automatically)
  • autobuild.htm (specifying_phenix_refine_parameters_12)
• find_domain
  • simple_ncs_from_pdb.htm (author_s__2)
  • find_ncs.htm (author_s__2)
• find_helices_strands
  • autobuild.htm (insert_helices)
  • find_helices_strands.htm
  • find_helices_strands.htm (author_s__2)
  • find_helices_strands.htm (purpose_2)
  • find_helices_strands.htm (how_find_helices_strands_finds_helices_and_strands_in_maps_)
• find_invariant_domain
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__9)
• find_invariant_domains
  • refinement.htm (find_invariant_domains)
  • simple_ncs_from_pdb.htm (find_invariant_domains)
  • multi_crystal_average.htm (find_invariant_domains)
• find_ncs
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • autosol.htm (use_ncs_in_denmod)
  • autosol.htm (find_ncs)
  • autobuild.htm (skip_ncs_in_model_building_and_refinement_2)
  • autobuild.htm (find_ncs)
• finer
  • phaser_mr.htm (anch1)
  • phaser_ep.htm (anch1)
• first_half
  • refinement.htm (mode_2)
  • refinement.htm (mode_3)
• first_macro_cycle_only
  • refinement.htm (mode)
• fisher
  • phenix-modules.htm (literature_2)
• fit_loops
  • autosol.htm (fit_loops)
  • autobuild.htm (connect)
  • autobuild.htm (fit_loops)
  • fit_loops.htm
  • fit_loops.htm (author_s__2)
• fit_phi_inc
  • ligandfit.htm (fit_phi_inc)
  • find_all_ligands.htm (fit_phi_inc)
• fit_phi_range
  • ligandfit.htm (fit_phi_range)
  • find_all_ligands.htm (fit_phi_range)
• fix_b_cart
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • refinement.htm (ignore_bulk_solvent_and_scale_failure)
• fix_b_sol
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • refinement.htm (fix_b_sol)
• fix_k_sol
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • refinement.htm (fix_k_sol)
• fix_rotamers
  • refinement.htm (fix_rotamers)
• fix_scale_for_calc_option
  • refinement.htm (fix_scale_for_calc_option)
• fix_wxc
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (fix_wxc)
• fix_wxu
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (fix_wxu)
• fix_xyz
  • autosol.htm (fix_xyz)
• fix_xyz_after_denmod
  • autosol.htm (fix_xyz_after_denmod)
• fixed_ensembleid_list
  • automr.htm
  • automr.htm (fixed_ensembleid_list)
  • automr.htm (fixed_euler_list)
  • automr.htm (fixed_frac_list)
• fixed_ensembles
  • automr.htm
  • automr.htm (use_all_plausible_sg)
• fixed_euler_list
  • automr.htm
  • automr.htm (fixed_ensembleid_list)
  • automr.htm (fixed_euler_list)
  • automr.htm (fixed_frac_list)
• fixed_frac_list
  • automr.htm
  • automr.htm (fixed_ensembleid_list)
  • automr.htm (fixed_euler_list)
  • automr.htm (fixed_frac_list)
• fixed_pdb
  • map_to_object.htm (how_phenix_map_to_object_works__2)
  • map_to_object.htm (standard_run_of_phenix_map_to_object__2)
  • map_to_object.htm
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
• fixscattfactors
  • autosol.htm (fixscattfactors)
• flags
  • faqs.htm
  • faqs.htm (what_is_an_r-free_flags_mismatch_)
  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • faqs.htm (how_do_i_run_autobuild_on_a_cluster__2)
  • faqs.htm
• flatness
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (score_type_list)
  • tutorial_mir.htm (statistical_density_modification_with_resolve_2)
  • tutorial_mad.htm (statistical_density_modification_with_resolve_2)
  • tutorial_sad.htm (statistical_density_modification_with_resolve_2)
• flattened
  • ligandfit.htm (how_the_ligandfit_wizard_works_5)
• flattening
  • faqs.htm
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__9)
  • tutorial_rebuild.htm (individual_rebuild-in-place_log_files__2)
• flexible
  • ligandfit.htm (purpose_of_the_ligandfit_wizard_3)
  • phaser.htm
  • phaser.htm (flexible_structure)
  • refine_gui.htm (atom_selection_2)
  • tutorial_ligandfit.htm
• flipping
  • validation.htm (all-atom_contacts_2)
• fmodel
  • refinement.htm (reflection_output_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
  • refinement.htm (developers_tools_2)
  • refinement.htm (export_final_f_model)
  • refinement.htm (pickle_fmodel)
• fobs_map
  • ligandfit.htm (lig_map_type)
  • find_all_ligands.htm (lig_map_type)
• fobs_mean
  • refinement.htm (fill_mode)
• fobs_mean_mixed_with_dfmodel
  • refinement.htm (fill_mode)
• fobs_minus_fobs_map
  • phenix_gui.htm (maps_2)
• fofc
  • refinement.htm (fofc)
  • autobuild.htm (output_files_from_autobuild_3)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_twin.htm (map_inspection_2)
• fofcwt
  • refinement.htm (mtz_label_amplitudes_2)
  • ligandfit.htm (sample_command_line_inputs_7)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• fofcwt_ml
  • refinement.htm (electron_density_maps_2)
• fom
  • refinement.htm (reflection_output_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_11)
  • autosol.htm (output_files_from_autosol_10)
  • autosol.htm
• force
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • refinement.htm (k_rep)
  • autosol.htm (sad_dataset_specifying_solvent_fraction_2)
  • autosol.htm (chain_type)
  • autobuild.htm (chain_type)
• force_anomalous_flag_to_be_equal_to
  • refinement.htm (refining_with_anomalous_data_or_what_phenix_refine_does_with_fobs_and_fobs-__2)
  • refinement.htm (force_anomalous_flag_to_be_equal_to)
  • refinement.htm (force_anomalous_flag_to_be_equal_to_1)
• force_combine_extend
  • autobuild.htm (force_combine_extend)
• force_ncs
  • find_ncs.htm (what_find_ncs_needs__10)
  • find_ncs.htm (force_ncs)
• form_factor_query
  • refinement.htm (f_and_f_refinement_2)
• formatting
  • faqs.htm (why_do_i_get_"_none_of_the_solve_versions_worked"_in_autosol__2)
  • refinement.htm (list_of_all_refinement_keywords_2)
  • autosol.htm (list_of_all_autosol_keywords_2)
  • autobuild.htm (list_of_all_autobuild_keywords_2)
  • ligandfit.htm (sample_command_line_inputs_10)
• fraction_aligned
  • tutorial_rebuild.htm (deciding_on_rebuild-in-place_and_editing_input_pdb_file_2)
• free_flags
  • refinement.htm (reflection_output_2)
• free_reflections_per_bin
  • refinement.htm (free_reflections_per_bin)
• freer_flag
  • faqs.htm
  • autosol.htm (input_refinement_labels)
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_5)
  • autobuild.htm (output_files_from_autobuild_3)
  • autobuild.htm (data)
• freer_flags
  • autosol.htm (display_labels)
  • autobuild.htm (output_files_from_autobuild_3)
  • autobuild.htm (display_labels)
  • ligandfit.htm (display_labels)
  • find_all_ligands.htm (display_labels)
• friendly
  • phaser_mr.htm (anch1)
• fully_skip_combine_extend
  • autobuild.htm (fully_skip_combine_extend)
• gamma
  • autosol.htm (unit_cell)
  • autobuild.htm (unit_cell)
  • ligandfit.htm (unit_cell)
  • automr.htm (unit_cell)
  • find_all_ligands.htm (unit_cell)
• gap_extension_penalty
  • superpose_pdbs.htm (gap_extension_penalty)
• gap_opening_penalty
  • superpose_pdbs.htm (gap_opening_penalty)
• gaussian
  • refinement.htm (scattering_factors_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_7)
  • elbow.htm (novice_options__136)
  • elbow.htm (novice_options__140)
  • tutorial_mir.htm (statistical_density_modification_with_resolve_2)
• general_positions_only
  • refinement.htm (general_positions_only)
  • refinement.htm (general_positions_only_1)
• geometries
  • phenix-modules.htm
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • autobuild.htm (including_ligand_coordinates_in_autobuild_3)
  • autobuild.htm (input_lig_file_list)
• geometry
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (random_seed_2)
• geometry_minimization
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • pdbtools.htm (max_fraction_of_distances_below_threshold)
• geometry_regularization
  • pdbtools.htm (anch1)
• geometry_restraints
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (definition_of_custom_bonds_and_angles_2)
  • refinement.htm (max_fraction_of_distances_below_threshold)
  • refinement.htm (sigma_1)
• get_cc_mtz_mtz
  • get_cc_mtz_mtz.htm
  • get_cc_mtz_mtz.htm (author_s__2)
  • get_cc_mtz_mtz.htm (purpose_2)
  • get_cc_mtz_mtz.htm (how_get_cc_mtz_mtz_works_)
  • get_cc_mtz_mtz.htm (how_get_cc_mtz_mtz_works__2)
• get_cc_mtz_pdb
  • get_cc_mtz_pdb.htm
  • get_cc_mtz_pdb.htm (author_s__2)
  • get_cc_mtz_pdb.htm (purpose_2)
  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works_)
  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works__2)
• get_dano
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (task)
  • xmanip.htm (output_label_root)
• get_diso
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (task)
  • xmanip.htm (input_data)
• get_lig_volume
  • ligandfit.htm (get_lig_volume)
  • find_all_ligands.htm (get_lig_volume)
• get_pdb
  • elbow.htm (additional_programs_2)
• get_smiles
  • elbow.htm (additional_programs_2)
• globally
  • refine_gui.htm (configuration_2)
• globulin
  • faqs.htm (what_sample_data_are_available_to_run_automatically__2)
  • examples.htm (what_sample_data_are_available_to_run_automatically__2)
  • tutorial_mr.htm
  • tutorial_mr.htm (introduction_2)
  • tutorial_mr.htm (running_the_demo_a2u-globulin-mr_data_with_automr)
• good_cc_hyss
  • autosol.htm (good_cc_hyss)
  • autosol.htm (best_of_n_hyss)
  • autosol.htm (best_of_n_hyss_always)
  • autosol.htm (min_fraction_of_sites_found)
• goto_run
  • running-wizards.htm (keeping_track_of_multiple_runs_of_a_wizard_from_the_gui__6)
  • running-wizards.htm (specific_limitations_and_problems__6)
• gradient
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (fofc)
  • tutorial_twin.htm (map_inspection_2)
• gradients_ratio
  • refinement.htm (target_weights)
• grid_resolution_factor
  • refinement.htm (electron_density_maps_2)
  • refinement.htm (grid_resolution_factor)
  • refinement.htm (grid_resolution_factor_1)
  • refinement.htm (grid_resolution_factor_2)
  • refinement.htm (grid_resolution_factor_3)
• grid_search
  • refinement.htm (target_weights)
• grid_search_scales
  • refinement.htm (grid_search_scales)
• grid_step
  • refinement.htm (grid_step)
• grid_step_factor
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • refinement.htm (grid_step_factor)
  • refinement.htm (grid_step_factor_1)
  • pdbtools.htm (grid_step_factor)
• group_adp
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (refinement_scenarios_2)
  • refinement.htm
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (strategy)
• group_adp_refinement_mode
  • refinement.htm
  • refinement.htm (group_adp_refinement_mode)
• group_anomalous
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (refinement_scenarios_2)
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (strategy)
  • refinement.htm (run_finite_differences_test_2)
• group_b_iso
  • refinement.htm (min_cubicle_edge)
• group_ca_length
  • autosol.htm (group_ca_length)
  • autobuild.htm (general_limitations_4)
  • autobuild.htm (group_ca_length)
  • find_helices_strands.htm (group_ca_length)
• group_labels_list
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • autosol.htm (group_labels_list)
• group_length
  • autosol.htm (group_length)
  • autobuild.htm (group_length)
• group_occupancy
  • refinement.htm (refine_ap_and_dp)
• group_search
  • ligandfit.htm (group_search)
  • find_all_ligands.htm (group_search)
• group_selection
  • refinement.htm
  • refinement.htm (group_adp_refinement_mode)
• groupings
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__7)
• h_bond_max
  • refinement.htm (h_bond_max)
• h_bond_min_mac
  • refinement.htm (h_bond_min_mac)
• h_bond_min_sol
  • refinement.htm (h_bond_min_sol)
• ha_iteration
  • autosol.htm (ha_iteration)
  • autosol.htm (phaser_completion)
• ha_sites_file
  • autosol.htm (ha_sites_file)
• halves
  • reflection_file_editor.htm (notes_on_usage_2)
• hand
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • autosol.htm (datasets_and_solutions_in_autosol__4)
  • autosol.htm (finding_heavy-atom_anomalously-scattering_atom_sites_3)
  • autosol.htm (running_autosol_separately_in_related_space_groups__2)
  • autosol.htm (scoring_of_heavy-atom_solutions_7)
• handedness
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_mad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_sad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• hands
  • autosol.htm (sad_dataset_reading_heavy-atom_sites_from_a_pdb_file_written_by_phenix_hyss_2)
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_mad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_sad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• have_hand
  • autosol.htm (sad_dataset_reading_heavy-atom_sites_from_a_pdb_file_written_by_phenix_hyss_2)
  • autosol.htm (have_hand)
• headd
  • what-is-phenix.htm (anch1_6)
  • faqs.htm (how_should_i_cite_phenix__2)
  • validation.htm (references_2)
• header
  • refinement.htm
  • refinement.htm (depositing_refined_structure_with_pdb_2)
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
  • old_gui.htm (strategies_8)
  • tutorial_mir.htm (what_parameters_did_i_use__2)
• headers
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
  • reel.htm (editing_7)
• heavily
  • create_maps.htm (guidelines_for_use_2)
• heavy_atom
  • autobuild.htm (run_autobuild_automatically_after_autosol_2)
• heavy_atom_search
  • autosol.htm (use_sca_as_is)
• height
  • refinement.htm (water_picking_2)
  • xtriage.htm (interpreting_xtriage_output_2)
  • phaser.htm (pseudo-translational_non-crystallographic_symmetry_2)
  • tutorial_mir.htm (running_phenix_xtriage_2)
  • tutorial_rebuild.htm (running_phenix_xtriage_2)
• helical
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___2)
  • autosol.htm (cc_helix_min)
  • autobuild.htm (cc_helix_min)
  • autobuild.htm (insert_helices)
  • find_helices_strands.htm (how_find_helices_strands_finds_helices_and_strands_in_maps__2)
• helices
  • autobuild.htm (how_the_autobuild_wizard_works_6)
  • autobuild.htm (standard_building_rebuild_in_place_and_multiple-models__2)
  • autobuild.htm (morph_an_mr_model_and_rebuild_it_2)
  • autobuild.htm (base_model)
  • autobuild.htm (dist_connect_max_helices)
• helices_before_trace
  • find_helices_strands.htm (helices_before_trace)
• helices_only
  • find_helices_strands.htm (helices_only)
• helices_strands_only
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___2)
  • autosol.htm (helices_strands_only)
  • autosol.htm (helices_strands_start)
  • autosol.htm (cc_helix_min)
  • autosol.htm (cc_strand_min)
• helices_strands_start
  • autosol.htm (helices_strands_start)
  • autobuild.htm (helices_strands_start)
  • tutorial_mir.htm (model-building_with_resolve_2)
  • tutorial_mad.htm (model-building_with_resolve_2)
• heme
  • autobuild.htm (general_limitations_4)
  • elbow.htm (novice_options__328)
  • elbow.htm (novice_options__332)
• hemihedral
  • tutorial_twin.htm (background_and_nomenclature_2)
  • tutorial_twin.htm (selection_of_a_cross_validation_set_2)
• hendrickson
  • refinement.htm (default_refinement_with_user_specified_x-ray_target_function_2)
  • refinement.htm (relevant_reading_2)
  • autosol.htm (sir__sad_datasets_5)
  • reflection_file_editor.htm (anch1)
  • tutorial_mir.htm
• hetatm
  • autobuild.htm (including_ligand_coordinates_in_autobuild_5)
  • autobuild.htm (general_limitations_4)
  • ligand_identification.htm (specific_limitations_and_problems__3)
  • tutorial_elbow.htm (generating_ligand_restraints_using_pdb_file_2)
• hexagonal
  • autosol.htm (running_autosol_separately_in_related_space_groups__2)
  • autosol.htm (specific_limitations_and_problems_7)
  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_9)
  • automr.htm (specific_limitations_and_problems_9)
• hexdigest
  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • autobuild.htm (skip_hexdigest)
• hexdigests
  • refinement.htm (ignore_pdb_hexdigest)
  • refinement.htm (ignore_pdb_hexdigest_1)
• high_res
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • autobuild.htm (and_optional_files_2)
• high_res_data
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
• high_resolution
  • faqs.htm
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (setting_the_resolution_range_for_the_refinement_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
• high_resolution_limit_to_include_scattering_from_h
  • refinement.htm (high_resolution_limit_to_include_scattering_from_h)
• highest_numbered
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_command-line_8)
• highest_resno
  • autobuild.htm (highest_resno)
  • autobuild.htm (edit_pdb)
• highest_resolution
  • refinement.htm (grid_step_factor)
  • refinement.htm (grid_step_factor_1)
  • pdbtools.htm (grid_step_factor)
• hires_file
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
  • autobuild.htm (and_optional_files_2)
  • autobuild.htm (merge_in_hires_data_2)
  • autobuild.htm (hires_file)
• hirshfeld
  • refinement.htm (relevant_reading_2)
  • refinement.htm (rigid_bond_test)
• hist_values
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  • pdbtools.htm (ignore_hydrogens)
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  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
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• hklout_type
  • xtriage.htm (hklout_type)
• hklperfect
  • autosol.htm (use_perfect)
  • autosol.htm (hklperfect)
  • autosol.htm (perfect_labels)
• hl_in_resolve
  • autosol.htm (hl_in_resolve)
• host
  • phenix_gui.htm (reporting_bugs_2)
• human_readable
  • reflection_file_tools.htm (phenix_mtz_dump_2)
• hydrogen
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (definition_of_custom_bonds_and_angles_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_12)
  • molprobity_tool.htm (usage_2)
• hydrogens
  • refinement.htm
  • refinement.htm
  • refinement.htm (hydrogens_in_refinement)
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_2)
• hyss
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (command_line_interface_3)
  • running-phenix.htm (tasks_and_strategies_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
• hyss_enable_early_termination
  • autosol.htm (hyss_enable_early_termination)
• hyss_general_positions_only
  • autosol.htm (hyss_general_positions_only)
• hyss_min_distance
  • autosol.htm (hyss_min_distance)
• hyss_n_fragments
  • autosol.htm (hyss_n_fragments)
• hyss_n_patterson_vectors
  • autosol.htm (hyss_n_patterson_vectors)
• hyss_random_seed
  • autosol.htm (hyss_random_seed)
• hyss_scoring
  • autosol.htm (skip_score_list)
• i_obs
  • xtriage.htm (interpreting_xtriage_output_2)
• i_ran_seed
  • autosol.htm (i_ran_seed)
  • autobuild.htm (specifying_phenix_refine_parameters_19)
  • autobuild.htm (i_ran_seed)
  • ligandfit.htm (i_ran_seed)
  • automr.htm (i_ran_seed)
• ias
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (ias)
  • refinement.htm (rmsd_cutoff_for_gradient_filtering)
• ias_b_iso_max
  • refinement.htm (ias_b_iso_max)
• ias_b_iso_min
  • refinement.htm (ias_b_iso_min)
• ias_occupancy_max
  • refinement.htm (ias_occupancy_max)
• ias_occupancy_min
  • refinement.htm (ias_occupancy_min)
• ice
  • phenix-modules.htm (data_analysis_3)
  • xtriage.htm (how_xtriage_works_2)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage_gui.htm
  • xtriage_gui.htm (data_quality_analyses_2)
• id_scale_ref
  • autosol.htm (id_scale_ref)
• ideal
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (xh_bond_distance_deviation_limit)
  • refinement.htm (lattice_symmetry_max_delta_2)
  • xtriage.htm (interpreting_xtriage_output_2)
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  • autosol.htm (hklperfect)
  • ligandfit.htm (what_the_ligandfit_wizard_needs_to_run_6)
• ignore_all_zeros
  • refinement.htm (ignore_all_zeros)
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  • ligandfit.htm (ignore_blanks)
  • automr.htm (ignore_blanks)
  • find_all_ligands.htm (ignore_blanks)
• ignore_bulk_solvent_and_scale_failure
  • refinement.htm (ignore_bulk_solvent_and_scale_failure)
• ignore_errors_in_subprocess
  • autobuild.htm (ignore_errors_in_subprocess)
• ignore_final_filtering_step
  • refinement.htm (ignore_final_filtering_step)
• ignore_hydrogens
  • refinement.htm (ignore_hydrogens)
  • refinement.htm (ignore_hydrogens_1)
  • pdbtools.htm (ignore_hydrogens)
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  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • refinement.htm (ignore_pdb_hexdigest)
  • refinement.htm (ignore_pdb_hexdigest_1)
• ignore_r_free_flags
  • refinement.htm (ignoring_test_free_flags_in_refinement_2)
  • refinement.htm (ignore_r_free_flags)
  • refinement.htm (ignore_r_free_flags_1)
• ignore_xn_free_r_mismatch
  • refinement.htm (ignore_xn_free_r_mismatch)
• ignore_zero_occupancy_atoms
  • refinement.htm (ignore_zero_occupancy_atoms)
  • refinement.htm (ignore_zero_occupancy_atoms_1)
  • pdbtools.htm (ignore_zero_occupancy_atoms)
• ignoring
  • refinement.htm
  • refinement.htm (ignoring_test_free_flags_in_refinement)
  • tutorial_mad.htm (scaling_mad_data_and_estimating_fa_values_2)
• ikeepflag
  • autosol.htm (ikeepflag)
• image_only_dm
  • faqs.htm
• images
  • phaser_mr.htm (additional_parameters_2)
• immormino
  • validation.htm (references_2)
• import
  • elbow.htm (purpose_4)
  • old_gui.htm (strategies_8)
  • tutorial_mir.htm (importrawdata___2)
  • tutorial_sad.htm (importrawdata___2)
• importrawdata
  • autosol.htm (change_sg)
  • tutorial_mir.htm
  • tutorial_mir.htm (importrawdata__)
  • tutorial_mir.htm (importrawdata___2)
  • tutorial_sad.htm
• impose
  • reflection_file_editor.htm (notes_on_usage_2)
• inano
  • autosol.htm (sir_dataset_3)
  • autosol.htm (inano)
  • autosol.htm (inano_list)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_2)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_5)
• inano_list
  • autosol.htm (inano_list)
• include_input_model
  • autobuild.htm (create_one_very_good_rebuilt_model_2)
  • autobuild.htm (include_input_model)
  • autobuild.htm (rebuild_in_place)
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  • automr.htm (include_input_model)
• include_molprobity
  • autobuild.htm (include_molprobity)
• individual_adp
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (refinement_scenarios_2)
  • refinement.htm
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
• individual_sites
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (refinement_scenarios_2)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
• individual_sites_real_space
  • refinement.htm (strategy)
• inflection
  • autosol.htm (wavelength_name_1)
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • hyss.htm (command_line_options_2)
  • tutorial_mad.htm (choosing_datafiles_with_high_signal-to-noise_2)
• influenced
  • create_maps.htm (guidelines_for_use_2)
• initial_geometry
  • elbow.htm (geometry_optimisation_2)
• initial_ias_occupancy
  • refinement.htm (initial_ias_occupancy)
• initial_model
  • tutorial_rebuild.htm
• initial_rms
  • refinement.htm (initial_rms)
  • simple_ncs_from_pdb.htm (initial_rms)
  • multi_crystal_average.htm (initial_rms)
• initial_velocities_zero_fraction
  • refinement.htm (initial_velocities_zero_fraction)
  • refinement.htm (initial_velocities_zero_fraction_1)
• input_compare_file
  • autosol.htm (input_compare_file)
  • autobuild.htm (input_compare_file)
• input_data
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (input_data)
• input_data_file
  • autobuild.htm (general_limitations_4)
  • autobuild.htm (refinement_file)
  • autobuild.htm (skip_hexdigest)
  • autobuild.htm (input_data_file)
  • ligandfit.htm (input_data_file)
• input_data_file_list
  • autosol.htm (group_labels_list)
• input_data_file_use
  • tutorial_mad.htm (generation_of_freer_flags_2)
• input_eff_file
  • autobuild.htm (specifying_phenix_refine_parameters_5)
  • autobuild.htm (specifying_phenix_refine_parameters_11)
• input_file
  • elbow.htm (purpose_4)
  • elbow.htm (pdb_input_2)
  • elbow.htm (smiles_input_2)
  • elbow.htm (other_input_2)
  • elbow.htm (geometry_optimisation_2)
• input_file_list
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • autosol.htm (input_file_list)
• input_files
  • autosol.htm (sequence)
  • autobuild.htm (sequence)
  • ligandfit.htm (ligand_format)
  • automr.htm (space_group)
  • find_all_ligands.htm (ligand_format)
• input_ha_file
  • autosol.htm (truncate_ha_sites_in_resolve)
  • autosol.htm (use_met_in_align)
  • autobuild.htm (truncate_density_at_heavy-atom_sites_2)
  • autobuild.htm (input_ha_file)
  • autobuild.htm (truncate_ha_sites_in_resolve)
• input_hires_file
  • autobuild.htm (skip_hexdigest)
  • tutorial_rebuild.htm (generation_of_freer_flags_2)
  • tutorial_build.htm (generation_of_freer_flags_2)
• input_hires_labels
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_5)
  • autobuild.htm (hires_file)
  • autobuild.htm (input_hires_labels)
• input_label_string
  • automr.htm (specifying_which_columns_of_data_to_use_from_input_data_files_4)
  • automr.htm (specifying_data_columns__3)
  • automr.htm (specifying_a_refinement_file_for_autobuild_3)
  • automr.htm (input_label_string)
  • automr.htm (display_labels)
• input_labels
  • faqs.htm (how_do_i_know_what_my_choices_of_labels_are_for_my_data_file__2)
  • faqs.htm
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_5)
  • autobuild.htm (general_limitations_4)
  • autobuild.htm (data)
• input_lig_file
  • ligandfit.htm (ligand_id)
  • ligandfit.htm (input_lig_file)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (additional_information_2)
  • find_all_ligands.htm (ligand_id)
• input_lig_file_list
  • faqs.htm
  • autosol.htm (sad_dataset_building_rna_instead_of_protein_2)
  • autosol.htm (chain_type)
  • autosol.htm (cif_def_file_list)
  • autosol.htm (ignore_blanks)
• input_ligand_compare_file
  • ligandfit.htm (input_ligand_compare_file)
  • find_all_ligands.htm (input_ligand_compare_file)
• input_map_file
  • autobuild.htm (data)
  • autobuild.htm (input_map_file)
  • tutorial_rebuild.htm (running_the_demo_a2u-globulin-rebuild_data_with_autobuild_2)
  • tutorial_rebuild.htm (summary_of_the_command-line_arguments_2)
  • tutorial_build.htm (running_the_demo_p9-build_data_with_autobuild_2)
• input_map_labels
  • faqs.htm (how_do_i_know_what_my_choices_of_labels_are_for_my_data_file__2)
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_5)
  • autobuild.htm (map_file)
  • autobuild.htm (input_map_labels)
  • tutorial_rebuild.htm (running_the_demo_a2u-globulin-rebuild_data_with_autobuild_2)
• input_ncs_file
  • autobuild.htm (run_autobuild_beginning_with_experimental_data_2)
  • autobuild.htm (find_ncs)
  • autobuild.htm (input_ncs_file)
• input_partial_model_file
  • ligandfit.htm (ligand_near_chain)
  • ligandfit.htm (ligand_near_res)
  • ligandfit.htm (input_partial_model_file)
  • find_all_ligands.htm (ligand_near_chain)
  • find_all_ligands.htm (ligand_near_res)
• input_partpdb_file
  • autosol.htm
  • autosol.htm (input_partpdb_file)
• input_pdb_file
  • autobuild.htm (input_pdb_file)
  • automr.htm (input_pdb_file)
  • tutorial_rebuild.htm (summary_of_the_command-line_arguments_2)
• input_phase_file
  • autosol.htm
  • autosol.htm (input_phase_file)
• input_phase_labels
  • autosol.htm
  • autosol.htm (input_phase_labels)
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_command-line_5)
• input_refinement_file
  • faqs.htm
  • autosol.htm (input_refinement_file)
  • autobuild.htm (run_autobuild_automatically_after_autosol_2)
  • autobuild.htm (data)
  • autobuild.htm (skip_hexdigest)
• input_refinement_labels
  • faqs.htm (how_do_i_know_what_my_choices_of_labels_are_for_my_data_file__2)
  • autosol.htm (input_refinement_labels)
  • autosol.htm (display_labels)
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_4)
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_5)
• input_seq_file
  • autosol.htm (input_seq_file)
  • autobuild.htm (input_seq_file)
  • automr.htm (input_seq_file)
  • tutorial_mr.htm (summary_of_the_command-line_arguments_2)
• input_seq_file_list
  • automr.htm (input_seq_file_list)
• insert_helices
  • autobuild.htm (dist_connect_max_helices)
  • autobuild.htm (n_ca_enough_helices)
  • autobuild.htm (insert_helices)
• installation
  • install.htm
  • install.htm (anch1)
  • install.htm (anch1_7)
  • phenix-environment.htm (setting_up_your_environment_2)
  • phenix-environment.htm (documentation_2)
• instructed
  • phaser_mr.htm (re-using_previous_results_2)
• intensities
  • refinement.htm (current_limitations_2)
  • refinement.htm (rejecting_reflections_by_sigma_2)
  • automr.htm (summary_of_inputs_and_outputs_for_automr_3)
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (interpreting_xtriage_output_2)
• intensity
  • phenix-modules.htm (literature_2)
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_7)
  • autobuild.htm (general_limitations_4)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage.htm (n_bins)
• interactions
  • phenix_gui.htm (preferences_2)
  • pdbtools.htm (anch1)
  • tutorial_ligandfit.htm (how_do_i_know_if_ligand_fitting_worked__2)
  • validation.htm (geometry_restraints_outliers_2)
• interatomic
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (relevant_reading_2)
  • refinement.htm (ias)
• interleaved_minimization
  • refinement.htm (verbose_6)
• interpolate
  • refinement.htm (interpolate)
  • refinement.htm (interpolate_1)
• interpolation
  • refinement.htm (interpolation)
• interpreter
  • ligandfit.htm (what_the_ligandfit_wizard_needs_to_run_7)
  • simple_ncs_from_pdb.htm (author_s__2)
  • find_ncs.htm (author_s__2)
  • running-wizards.htm (basic_operation_of_a_wizard_from_the_command-line_5)
  • xtriage.htm (author_s__2)
• inverse
  • autosol.htm (running_autosol_separately_in_related_space_groups__2)
  • tutorial_mir.htm (reading_the_datafiles__2)
  • tutorial_mir.htm (importrawdata___2)
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_mir.htm
• iobs
  • refinement.htm (current_limitations_2)
  • refinement.htm (rejecting_reflections_by_sigma_2)
  • xtriage.htm (interpreting_xtriage_output_2)
• iotbx
  • running-wizards.htm (keeping_track_of_multiple_runs_of_a_wizard_from_the_command-line_5)
  • explore_metric_symmetry.htm (purpose_2)
  • explore_metric_symmetry.htm (keywords_2)
  • explore_metric_symmetry.htm (examples_2)
• irex
  • refinement.htm (trajectory_directory)
• irexp
  • refinement.htm (trajectory_directory)
  • refinement.htm (irexp)
• isigi_cut
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (isigi_cut)
  • xtriage.htm (completeness_cut)
• isizeit
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
• isomesh
  • pymol.htm (useful_pymol_commands_2)
• isosurface
  • refine_gui.htm (acknowledgements_2)
• isotropic
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm (available_features_2)
  • refinement.htm
  • refinement.htm (occupancy_refinement_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
• iterative_build_omit
  • autobuild.htm (make_an_iterative-build_omit_map_around_atoms_in_target_pdb_2)
  • autobuild.htm (composite_omit_type)
• jiffy_result
  • xmanip.htm (examples_2)
• join_cif_files
  • elbow.htm (additional_programs_2)
• join_mol2_files
  • elbow.htm (additional_programs_2)
• join_pdb_files
  • elbow.htm (additional_programs_2)
• k_overall
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (k_overall)
• k_rep
  • refinement.htm (trajectory_directory)
  • refinement.htm (k_rep)
• k_sol
  • refinement.htm (reflection_output_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
  • refinement.htm (developers_tools_2)
  • refinement.htm (k_sol)
  • xmanip.htm (command_line_interface_2)
• k_sol_b_sol_grid_search
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_2)
  • refinement.htm (k_sol_b_sol_grid_search)
• k_sol_grid_search_max
  • refinement.htm (k_sol_grid_search_max)
• k_sol_grid_search_min
  • refinement.htm (k_sol_grid_search_min)
• k_sol_max
  • refinement.htm (k_sol_max)
• k_sol_min
  • refinement.htm (k_sol_min)
• k_sol_step
  • refinement.htm (k_sol_step)
• keedy
  • validation.htm (references_2)
• keep_f_mag
  • get_cc_mtz_mtz.htm (how_get_cc_mtz_mtz_works__2)
  • get_cc_mtz_mtz.htm (specific_limitations_and_problems__2)
  • get_cc_mtz_mtz.htm (keep_f_mag)
• keep_input_ligands
  • autobuild.htm (including_ligand_coordinates_in_autobuild_3)
  • autobuild.htm (general_limitations_3)
  • autobuild.htm (keep_input_ligands)
• keep_input_waters
  • autobuild.htm (keeping_waters_from_your_input_file_in_autobuild_3)
  • autobuild.htm (including_ligand_coordinates_in_autobuild_3)
  • autobuild.htm (general_limitations_3)
  • autobuild.htm (keep_input_waters)
• keep_pdb_atoms
  • autobuild.htm (keeping_waters_from_your_input_file_in_autobuild_3)
  • autobuild.htm (general_limitations_4)
  • autobuild.htm (keep_input_waters)
  • autobuild.htm (keep_pdb_atoms)
• kernel_on_chebyshev_nodes
  • refinement.htm (kernel_on_chebyshev_nodes)
• kernel_width_free_reflections
  • refinement.htm (kernel_width_free_reflections)
• kick_map
  • refinement.htm (space_group_1)
• kick_size
  • refinement.htm (kick_size)
• kinemage
  • hydrogens.htm (anch1)
  • tutorial_molprobity.htm (anch1)
• label_appendix
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (label_appendix)
• label_extension
  • xtriage.htm (label_extension)
• labin_use
  • tutorial_mad.htm (generation_of_freer_flags_2)
• lattice
  • refinement.htm
  • refinement.htm (lattice_symmetry_max_delta_2)
  • refinement.htm (use_lattice_symmetry_2)
  • autosol.htm (r_free_flags_use_lattice_symmetry)
  • autosol.htm (r_free_flags_lattice_symmetry_max_delta)
• lattice_symmetry_max_delta
  • refinement.htm (lattice_symmetry_max_delta)
  • refinement.htm (lattice_symmetry_max_delta_1)
  • refinement.htm (lattice_symmetry_max_delta_2)
  • reflection_statistics.htm (anch1)
• lbfgs
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_with_all_default_parameters_2)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (random_seed_2)
  • refinement.htm (relevant_reading_2)
• lbfgs_line_search_max_function_evaluations
  • refinement.htm (lbfgs_line_search_max_function_evaluations)
• lbfgs_max_iterations
  • refinement.htm (lbfgs_max_iterations)
• lebedev
  • phenix-modules.htm (literature_2)
  • refinement.htm (relevant_reading_2)
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_twin.htm (examples_2)
• libraries
  • what-is-phenix.htm (anch1_2)
  • autosol.htm (specific_limitations_and_problems_7)
  • autobuild.htm (standard_building_rebuild_in_place_and_multiple-models__2)
  • autobuild.htm (specific_limitations_and_problems_2)
  • autobuild.htm (track_libs)
• lig_id
  • ligand_identification.htm (list_of_ligands_in_the_phenix_ligand_identification_library_3)
• lig_map_type
  • ligandfit.htm (sample_command_line_inputs_3)
  • ligandfit.htm (sample_command_line_inputs_4)
  • ligandfit.htm (lig_map_type)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (lig_map_type)
• lig_volume
  • tutorial_ligandfit.htm (the_ligandfit_summary_dat_summary_file_2)
• ligand
  • what-is-phenix.htm (anch1_3)
  • running-phenix.htm (tasks_and_strategies_3)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm
  • phenix-modules.htm (automated_ligand_density_analysis)
• ligand_cc_min
  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
  • ligandfit.htm (ligand_cc_min)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (ligand_cc_min)
• ligand_completeness_min
  • ligandfit.htm (ligand_completeness_min)
  • find_all_ligands.htm (ligand_completeness_min)
• ligand_file
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
• ligand_format
  • ligandfit.htm (ligand_format)
  • find_all_ligands.htm (ligand_format)
• ligand_id
  • ligandfit.htm (ligand_id)
  • find_all_ligands.htm (ligand_id)
• ligand_list
  • ligandfit.htm (sample_command_line_inputs_8)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (ligand_list)
• ligand_near_chain
  • ligandfit.htm (sample_command_line_inputs_9)
  • ligandfit.htm (ligand_near_chain)
  • ligandfit.htm (ligand_near_res)
  • find_all_ligands.htm (ligand_near_chain)
  • find_all_ligands.htm (ligand_near_res)
• ligand_near_pdb
  • ligandfit.htm (ligand_near_pdb)
  • find_all_ligands.htm (ligand_near_pdb)
• ligand_near_res
  • ligandfit.htm (sample_command_line_inputs_9)
  • ligandfit.htm (specific_limitations_and_problems_7)
  • ligandfit.htm (ligand_near_chain)
  • ligandfit.htm (ligand_near_res)
  • find_all_ligands.htm (ligand_near_chain)
• ligand_start
  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
  • ligandfit.htm (sample_command_line_inputs_10)
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_command-line_12)
• ligandfit
  • what-is-phenix.htm (anch1_3)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_ligand_density_analysis_3)
  • autosol.htm (trace_as_lig)
  • autobuild.htm (trace_as_lig)
• ligandfit_facts
  • ligandfit.htm (output_files_from_ligandfit_5)
• ligandfit_lores
  • tutorial_ligandfit.htm (what_parameters_did_i_use__2)
• ligandfit_summary
  • ligandfit.htm (output_files_from_ligandfit_4)
  • tutorial_ligandfit.htm
  • tutorial_ligandfit.htm (the_ligandfit_summary_dat_summary_file)
  • tutorial_ligandfit.htm (the_ligandfit_summary_dat_summary_file_2)
• ligandfit_warnings
  • ligandfit.htm (output_files_from_ligandfit_6)
• likelihood
  • what-is-phenix.htm (anch1_2)
  • phenix-modules.htm (data_analysis_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • phenix-modules.htm (structure_refinement_3)
  • phenix-modules.htm (literature_2)
• likelihood_weighted
  • refinement.htm (electron_density_maps_2)
  • refinement.htm (likelihood_weighted)
  • refinement.htm (likelihood_weighted_1)
  • refinement.htm (likelihood_weighted_2)
  • refinement.htm (likelihood_weighted_3)
• link_distance_cutoff
  • refinement.htm (link_distance_cutoff)
  • autosol.htm (link_distance_cutoff)
  • autobuild.htm (specifying_phenix_refine_parameters_36)
  • autobuild.htm (specifying_phenix_refine_parameters_37)
  • autobuild.htm (link_distance_cutoff)
• link_edits
  • elbow.htm (additional_programs_2)
  • tutorial_elbow.htm (generating_link_edits_2)
• link_to_edits
  • ready_set.htm (link_to_edits)
• local_real_space_fit_angular_step
  • refinement.htm (local_real_space_fit_angular_step)
• local_scaling
  • tutorial_twin.htm (map_inspection_2)
• local_search
  • ligandfit.htm (local_search)
  • ligandfit.htm (search_dist)
  • find_all_ligands.htm (local_search)
  • find_all_ligands.htm (search_dist)
• localscale_before_phaser
  • autosol.htm (localscale_before_phaser)
• localscaling
  • autosol.htm (localscale_before_phaser)
  • tutorial_mir.htm (scaling_mir_data_2)
  • tutorial_mad.htm (scaling_mad_data_and_estimating_fa_values_2)
• log_denmod
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• log_eval
  • autobuild.htm (output_files_from_autobuild_3)
  • tutorial_mir.htm (model-building_with_resolve_2)
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• log_refine
  • autobuild.htm (output_files_from_autobuild_3)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• logfile
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (log)
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (logfile)
• loop_cc_min
  • autosol.htm (loop_cc_min)
  • autobuild.htm (loop_cc_min)
  • fit_loops.htm (standard_run_of_fit_loops__2)
  • fit_loops.htm (loop_cc_min)
• lovell
  • autobuild.htm (richardson_rotamers)
  • molprobity_tool.htm (literature_2)
• low_resolution
  • refinement.htm (running_phenix_refine_2)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (water_picking_2)
  • refinement.htm (setting_the_resolution_range_for_the_refinement_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
• ls_target_names
  • refinement.htm (scaling)
• ls_wexp_k1
  • refinement.htm (target_name)
• ls_wexp_k2
  • refinement.htm (target_name)
• ls_wexp_kunit
  • refinement.htm (target_name)
• ls_wff_k1
  • refinement.htm (target_name)
• ls_wff_k1_fixed
  • refinement.htm (target_name)
• ls_wff_k1ask3_fixed
  • refinement.htm (target_name)
• ls_wff_k2
  • refinement.htm (target_name)
• ls_wff_kunit
  • refinement.htm (target_name)
• ls_wunit_k1
  • refinement.htm (target_1)
  • refinement.htm (target_2)
  • refinement.htm (target_name)
• ls_wunit_k1_fixed
  • refinement.htm (target_name)
• ls_wunit_k1ask3_fixed
  • refinement.htm (target_name)
• ls_wunit_k2
  • refinement.htm (target_name)
• ls_wunit_kunit
  • refinement.htm (target_name)
• lsm_k1
  • refinement.htm (target_name)
• lsm_k1_fixed
  • refinement.htm (target_name)
• lsm_k1ask3_fixed
  • refinement.htm (target_name)
• lsm_k2
  • refinement.htm (target_name)
• lsm_kunit
  • refinement.htm (target_name)
• lsq_scale
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (task)
  • xmanip.htm (scale_weight)
• m_dtfo_d_fc
  • refinement.htm (fofc)
  • tutorial_twin.htm (map_inspection_2)
• m_gradient
  • refinement.htm (fofc)
  • tutorial_twin.htm (map_inspection_2)
• m_isym
  • autosol.htm (datafile_formats_in_autosol_3)
• machine_readable
  • reflection_file_tools.htm (phenix_mtz_dump_2)
• macro_cycle
  • refinement.htm (refinement_of_coordinates_2)
• macro_cycles
  • pdbtools.htm (macro_cycles)
• macrocycle
  • refinement.htm (mode)
• macrocycles
  • refinement.htm (refinement_with_all_default_parameters_2)
• mad
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (literature_2)
  • faqs.htm (what_sample_data_are_available_to_run_automatically__2)
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • refinement.htm (f_and_f_refinement_2)
• mad_ha_add_f_double_prime_list
  • autosol.htm (sad_with_more_than_one_anomalously-scattering_atom__3)
  • autosol.htm (mad_ha_add_f_double_prime_list)
  • autosol.htm (mad_ha_add_f_prime_list)
  • autosol.htm (mad_ha_add_list)
• mad_ha_add_f_prime_list
  • autosol.htm (sad_with_more_than_one_anomalously-scattering_atom__3)
  • autosol.htm (mad_ha_add_f_double_prime_list)
  • autosol.htm (mad_ha_add_f_prime_list)
  • autosol.htm (mad_ha_add_list)
• mad_ha_add_list
  • autosol.htm (sad_with_more_than_one_anomalously-scattering_atom__3)
  • autosol.htm (atom_type_1)
  • autosol.htm (mad_ha_type)
  • autosol.htm (mad_ha_add_f_double_prime_list)
  • autosol.htm (mad_ha_add_f_prime_list)
• mad_ha_n
  • autosol.htm (mad_ha_n)
• mad_ha_type
  • autosol.htm (mad_ha_type)
  • autosol.htm (mad_ha_add_list)
• mad_scale
  • reflection_file_tools.htm (phenix_cns_as_mtz_2)
• mahalanobis
  • xtriage.htm (interpreting_xtriage_output_2)
• mandatory
  • phaser_mr.htm
  • phaser_mr.htm (input_files_and_mandatory_parameters)
  • phaser_ep.htm
  • phaser_ep.htm (input_files_and_mandatory_parameters)
• manipulate_miller
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (action)
  • xmanip.htm (user_supplied_law)
• manipulate_pdb
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (action)
  • xmanip.htm (show_instructions)
• map_coeff_labin_list
  • multi_crystal_average.htm (map_coeff_labin_list)
• map_coeff_list
  • multi_crystal_average.htm (output_files_from_phenix_multi_crystal_average_2)
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__2)
  • multi_crystal_average.htm (map_coeff_list)
• map_coefficients
  • autobuild.htm (output_files_from_autobuild_3)
• map_coefficients_format
  • refinement.htm (map_coefficients_format)
• map_coeffs
  • autobuild.htm (specifying_other_general_parameters_3)
  • automr.htm (output_files_from_automr_7)
  • automr.htm (output_files_from_automr_8)
  • find_helices_strands.htm (standard_run_of_find_helices_strands__2)
  • find_helices_strands.htm (standard_run_of_find_helices_strands__3)
• map_cutoff
  • refinement.htm (map_cutoff)
• map_file
  • faqs.htm
  • faqs.htm
  • autobuild.htm (and_optional_files_2)
  • autobuild.htm (specifying_other_general_parameters_3)
  • autobuild.htm (map_file)
• map_format
  • refinement.htm (map_format)
• map_next_to_model
  • refinement.htm (water_picking_2)
  • refinement.htm (max_number_of_peaks)
  • refinement.htm (max_number_of_peaks_1)
• map_to_object
  • map_to_object.htm
  • map_to_object.htm (author_s__2)
  • map_to_object.htm (purpose_2)
  • map_to_object.htm (how_phenix_map_to_object_works_)
  • map_to_object.htm (how_phenix_map_to_object_works__2)
• map_type
  • refinement.htm (map_type)
  • refinement.htm (map_type_1)
• map_types
  • refinement.htm (refinement_using_twinned_data_2)
  • refinement.htm (mode_5)
  • tutorial_twin.htm (map_inspection_2)
• maps_only
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
  • faqs.htm (how_can_i_specify_a_mask_for_density_modification_in_autosol_autobuild__2)
  • autobuild.htm (density-modify_with_or_without_a_model_and_make_maps__2)
  • autobuild.htm (calculate_a_prime-and-switch_map__2)
  • autobuild.htm (maps_only)
• mask_cycles
  • autosol.htm (mask_cycles)
  • multi_crystal_average.htm (mask_cycles)
• mask_type
  • autosol.htm (mask_type)
  • autobuild.htm (mask_type)
  • tutorial_mir.htm
• massage
  • xtriage.htm (completeness_cut)
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• master_params
  • doc_procedures.htm (generating_current_phenix_html_documents_2)
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
• match_radius
  • refinement.htm (match_radius)
  • simple_ncs_from_pdb.htm (match_radius)
  • multi_crystal_average.htm (match_radius)
• matthews
  • xtriage.htm (how_xtriage_works_2)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (n_copies_per_asu)
• max_cc_extra_unique_solutions
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_extra_unique_solutions)
• max_choices
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_choices)
  • autosol.htm (max_extra_unique_solutions)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (what_to_do_next_2)
• max_composite_choices
  • autosol.htm (max_composite_choices)
  • tutorial_mir.htm (what_to_do_next_2)
• max_d_min
  • refinement.htm (max_d_min)
• max_delta
  • explore_metric_symmetry.htm (keywords_2)
• max_extra_unique_solutions
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_extra_unique_solutions)
• max_fraction_of_distances_below_threshold
  • refinement.htm (max_fraction_of_distances_below_threshold)
  • pdbtools.htm (max_fraction_of_distances_below_threshold)
• max_free
  • refinement.htm (creating_r-free_flags_if_not_present_in_the_input_reflection_files__2)
  • refinement.htm (max_free)
  • refinement.htm (max_free_1)
  • refinement.htm (max_free_2)
• max_ha_iterations
  • autosol.htm (max_ha_iterations)
• max_iterations
  • refinement.htm (max_iterations)
  • refinement.htm (max_iterations_1)
  • pdbtools.htm (max_iterations)
• max_low_high_res_limit
  • refinement.htm (max_low_high_res_limit)
• max_model_peak_dist
  • refinement.htm (water_picking_2)
  • refinement.htm (max_model_peak_dist)
  • refinement.htm (max_model_peak_dist_1)
• max_number_of_distances_below_threshold
  • refinement.htm (max_number_of_distances_below_threshold)
  • pdbtools.htm (max_number_of_distances_below_threshold)
• max_number_of_iterations
  • refinement.htm (changing_the_number_of_refinement_cycles_and_minimizer_iterations_2)
  • refinement.htm (max_number_of_iterations)
  • refinement.htm (max_number_of_iterations_1)
  • refinement.htm (max_number_of_iterations_2)
  • refinement.htm (max_number_of_iterations_3)
• max_number_of_peaks
  • refinement.htm (max_number_of_peaks)
  • refinement.htm (max_number_of_peaks_1)
• max_number_of_resolution_bins
  • refinement.htm (max_number_of_resolution_bins)
• max_occ
  • autobuild.htm (specifying_phenix_refine_parameters_31)
  • autobuild.htm (max_occ)
• max_order
  • explore_metric_symmetry.htm (keywords_2)
• max_peaks
  • refinement.htm (max_peaks)
  • refinement.htm (max_peaks_1)
• max_range_to_keep
  • autosol.htm (max_range_to_keep)
• max_reasonable_bond_distance
  • refinement.htm (max_reasonable_bond_distance)
  • pdbtools.htm (max_reasonable_bond_distance)
• max_rmsd
  • refinement.htm (max_rmsd)
  • simple_ncs_from_pdb.htm (how_simple_ncs_from_pdb_works__5)
  • simple_ncs_from_pdb.htm (max_rmsd)
  • multi_crystal_average.htm (max_rmsd)
• max_rmsd_domain
  • refinement.htm (max_rmsd_domain)
  • simple_ncs_from_pdb.htm (max_rmsd_domain)
  • multi_crystal_average.htm (max_rmsd_domain)
• max_rmsd_use
  • simple_ncs_from_pdb.htm (specific_limitations_and_problems__3)
• max_rmsd_user
  • refinement.htm (max_rmsd_user)
  • simple_ncs_from_pdb.htm (max_rmsd_user)
  • multi_crystal_average.htm (max_rmsd_user)
• max_rotomer_distortion
  • refinement.htm (max_rotomer_distortion)
  • pdbtools.htm (max_rotomer_distortion)
• max_single_sites
  • autosol.htm (max_single_sites)
• max_wait_time
  • autosol.htm (max_wait_time)
  • autobuild.htm (max_wait_time)
  • ligandfit.htm (max_wait_time)
  • automr.htm (max_wait_time)
  • find_all_ligands.htm (max_wait_time)
• maximally
  • refinement.htm (max_rotomer_distortion)
  • pdbtools.htm (max_rotomer_distortion)
• maximize
  • refinement.htm (maximize_size_of_groups)
  • autosol.htm (scoring_of_heavy-atom_solutions_12)
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__7)
  • simple_ncs_from_pdb.htm (maximize_size_of_groups)
  • multi_crystal_average.htm (maximize_size_of_groups)
• maximize_size_of_groups
  • refinement.htm (maximize_size_of_groups)
  • simple_ncs_from_pdb.htm (maximize_size_of_groups)
  • multi_crystal_average.htm (specific_limitations_and_problems__2)
  • multi_crystal_average.htm (maximize_size_of_groups)
• maximizes
  • autobuild.htm (morph_an_mr_model_and_rebuild_it_2)
  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works__2)
  • get_cc_mtz_mtz.htm (how_get_cc_mtz_mtz_works__2)
  • tutorial_mir.htm
• maximizing
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__6)
• mbp_anom_diffs
  • hyss.htm (if_things_go_wrong_2)
• mean_random_solution_score
  • autosol.htm (scoring_of_heavy-atom_solutions_4)
• mean_shift_for_mask_update
  • refinement.htm (mean_shift_for_mask_update)
  • refinement.htm (mean_shift_for_mask_update_1)
  • pdbtools.htm (mean_shift_for_mask_update)
• merge_models
  • faqs.htm
  • autobuild.htm (merge_models)
• metal_coordination
  • elbow.htm (additional_programs_2)
  • ready_set.htm (link_to_edits)
  • tutorial_elbow.htm (metal_coordination_2)
• methionines
  • tutorial_mad.htm (guessing_cell_contents_2)
  • tutorial_sad.htm (guessing_cell_contents_2)
• miller_array
  • xmanip.htm (b_sol)
• min_cc_res_rebuild
  • autobuild.htm (touch_up_a_model__2)
  • autobuild.htm (min_cc_res_rebuild)
  • autobuild.htm (worst_percent_res_rebuild)
• min_cc_residue_rebuild
  • autobuild.htm (touch_up)
• min_contig_length
  • refinement.htm (min_contig_length)
  • simple_ncs_from_pdb.htm (min_contig_length)
  • multi_crystal_average.htm (min_contig_length)
• min_cross_distance
  • refinement.htm (min_cross_distance)
  • refinement.htm (min_cross_distance_1)
• min_cubicle_edge
  • refinement.htm (min_cubicle_edge)
  • refinement.htm (min_cubicle_edge_1)
• min_distance_sym_equiv
  • refinement.htm (min_distance_sym_equiv)
  • refinement.htm (min_distance_sym_equiv_1)
• min_fom
  • autosol.htm (min_fom)
• min_fom_for_dm
  • autosol.htm (min_fom_for_dm)
• min_fraction_domain
  • refinement.htm (min_fraction_domain)
  • simple_ncs_from_pdb.htm (min_fraction_domain)
  • multi_crystal_average.htm (min_fraction_domain)
• min_fraction_of_sites_found
  • autosol.htm (good_cc_hyss)
  • autosol.htm (best_of_n_hyss)
  • autosol.htm (best_of_n_hyss_always)
  • autosol.htm (min_fraction_of_sites_found)
• min_hyss_cc
  • autosol.htm (min_hyss_cc)
• min_iterations
  • refinement.htm (min_iterations)
• min_length
  • refinement.htm (min_length)
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__8)
  • simple_ncs_from_pdb.htm (min_length)
  • multi_crystal_average.htm (min_length)
• min_length_recursion
  • refinement.htm (min_length_recursion)
  • simple_ncs_from_pdb.htm (min_length_recursion)
  • multi_crystal_average.htm (min_length_recursion)
• min_model_peak_dist
  • refinement.htm (water_picking_2)
  • refinement.htm (min_model_peak_dist)
  • refinement.htm (min_model_peak_dist_1)
• min_number_of_reflections
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (min_number_of_reflections)
• min_number_of_test_set_reflections_for_max_likelihood_targe
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  • refinement.htm (hydrogens_in_refinement_2)
  • ready_set.htm (perdeuterate)
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• perfect_map_coeff_labin_list
  • multi_crystal_average.htm (perfect_map_coeff_labin_list)
• perfect_map_coeff_list
  • multi_crystal_average.htm (perfect_map_coeff_list)
• perform_analyses
  • xtriage.htm (perform_analyses)
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  • xtriage.htm (standard_run_of_xtriage_2)
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  • xtriage.htm (xtriage_keywords_in_detail_2)
• periodic
  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
• permutations
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• personally
  • phenix_gui.htm (reporting_bugs_2)
• perturbations
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• ph2fofcwt_ml
  • refinement.htm (electron_density_maps_2)
• ph2fofcwt_no_fill
  • refinement.htm (mtz_label_phases_3)
• phase_full_resolution
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  • autosol.htm (phase_full_resolution)
• phaser
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (tasks_and_strategies_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • faqs.htm (where_can_i_find_sample_data__2)
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  • autosol.htm (phaser_completion)
• phaser_keywords
  • phaser_mr.htm (additional_parameters_2)
• phasing_method
  • autosol.htm (phasing_method)
• phdelfwt
  • faqs.htm (why_doesnt_coot_recognize_my_mtz_file_from_autobuild___2)
• phenix_documentation
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
• phenix_env
  • phenix-environment.htm (setting_up_your_environment_2)
  • tutorial_mir.htm (setting_up_to_run_phenix_2)
  • tutorial_mr.htm (setting_up_to_run_phenix_2)
  • tutorial_ligandfit.htm (setting_up_to_run_phenix_2)
  • tutorial_rebuild.htm (setting_up_to_run_phenix_2)
• phenix_environment
  • phenix-environment.htm (setting_up_your_environment_2)
• phenix_examples
  • find_helices_strands.htm (standard_run_of_find_helices_strands__3)
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
  • tutorial_build.htm (model-building_with_resolve_2)
  • tutorial_build.htm (creating_an_improved_model_after_autobuild_2)
• phenix_html
  • doc_procedures.htm (generating_current_phenix_html_documents_2)
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
• phenix_installer_date
  • phenix-environment.htm (setting_up_your_environment_2)
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  • phenix-environment.htm (setting_up_your_environment_2)
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  • phenix-environment.htm (setting_up_your_environment_2)
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  • phenix-environment.htm (setting_up_your_environment_2)
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  • phenix-environment.htm (setting_up_your_environment_2)
• phfofcwt_ml
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• pickle_fmodel
  • refinement.htm (pickle_fmodel)
• pipeline
  • phaser_ep.htm (anch1)
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  • autosol.htm (place_waters)
  • autobuild.htm (picking_waters_in_autobuild_4)
  • autobuild.htm (keeping_waters_from_your_input_file_in_autobuild_3)
  • autobuild.htm (specifying_phenix_refine_parameters_21)
  • autobuild.htm (keep_input_waters)
• place_waters_in_combine
  • autobuild.htm (specifying_phenix_refine_parameters_23)
  • autobuild.htm (place_waters_in_combine)
• plain_pairs_radius
  • refinement.htm (plain_pairs_radius)
• planar
  • validation.htm (geometry_restraints_outliers_2)
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  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (planarities)
  • pdbtools.htm (anch1)
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  • refinement.htm (planarity_restraints_sorted_by_residual)
  • pdbtools.htm (planarity_restraints_sorted_by_residual)
• plugins
  • phenix_gui.htm (model_tools_2)
• poor_cc_threshold
  • refinement.htm (poor_cc_threshold)
• poor_map_value_threshold
  • refinement.htm (poor_map_value_threshold)
• pre_calculated_map_coeffs
  • ligandfit.htm (sample_command_line_inputs_4)
  • ligandfit.htm (lig_map_type)
  • find_all_ligands.htm (lig_map_type)
• precalculated
  • create_maps.htm (guidelines_for_use_2)
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  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (specify_the_name_for_output_files_2)
  • refinement.htm (prefix)
  • automr.htm (specifying_a_refinement_file_for_autobuild_3)
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  • phenix_gui.htm (utilities_2)
  • phaser_mr.htm (anch1)
• preserve
  • reflection_file_editor.htm (dealing_with_r-free_flags_2)
• primary_map_cutoff
  • refinement.htm (water_picking_2)
  • refinement.htm (primary_map_cutoff)
• primary_map_type
  • refinement.htm (water_picking_2)
  • refinement.htm (primary_map_type)
• prime_and_switch
  • autobuild.htm (calculate_a_prime-and-switch_map__2)
• primitive_setting
  • xmanip.htm (standard_laws)
• print_sequence
  • elbow.htm (additional_programs_2)
• probabilistic
  • xtriage.htm (how_xtriage_works_2)
• proceed_with_excessive_length_bonds
  • refinement.htm (proceed_with_excessive_length_bonds)
  • pdbtools.htm (proceed_with_excessive_length_bonds)
• processors
  • faqs.htm (how_do_i_run_autobuild_on_a_cluster__2)
  • faqs.htm (autobuild_seems_to_be_taking_a_long_time_what_is_the_usual_time_for_a_run__2)
  • autosol.htm (nproc)
  • autosol.htm (nbatch)
  • autobuild.htm
• prolsq_repulsion_function_changes
  • refinement.htm (trajectory_directory)
• prot_seq_file
  • automr.htm (weight_seq_list)
• protocol
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (water_picking_2)
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (min_number_of_reflections)
• ps_in_rebuild
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
  • autobuild.htm (calculate_a_prime-and-switch_map__2)
  • autobuild.htm (ps_in_rebuild)
• pseudomerohedral
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_twin.htm (examples_2)
• pseudosymmetry
  • xtriage_gui.htm (twinning_analyses_2)
• pseudotranslation
  • xtriage_gui.htm (interpreting_xtriage_output_2)
  • tutorial_mir.htm (running_phenix_xtriage_2)
  • tutorial_rebuild.htm (running_phenix_xtriage_2)
  • tutorial_build.htm (running_phenix_xtriage_2)
  • tutorial_mad.htm (running_phenix_xtriage_2)
• publications
  • what-is-phenix.htm (anch1_6)
• pulchra
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
  • find_helices_strands.htm (pulchra)
  • phenix_gui.htm (building_and_refinement_2)
• put_into_box_with_buffer
  • pdbtools.htm (put_into_box_with_buffer)
• qsub
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  • autosol.htm (background)
  • autosol.htm (run_command)
  • autobuild.htm
  • autobuild.htm (background)
• quality_factor
  • refinement.htm (quality_factor)
  • refinement.htm (quality_factor_1)
  • pdbtools.htm (quality_factor)
• quantum
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • elbow.htm (purpose_2)
  • elbow.htm (novice_options__122)
  • elbow.htm (novice_options__128)
  • elbow.htm (novice_options__134)
• queue
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  • autosol.htm (run_command)
  • autobuild.htm (background)
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  • ligandfit.htm (background)
• quick_clashlist
  • molprobity_tool.htm (usage_2)
• r32
  • autosol.htm (specific_limitations_and_problems_7)
  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_9)
  • automr.htm (specific_limitations_and_problems_9)
  • running-wizards.htm (specific_limitations_and_problems__7)
• r32_hexagonal_setting
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• r_abs_twin
  • xtriage.htm (interpreting_xtriage_output_2)
• r_free
  • refinement_examples.htm (examples_2)
• r_free_flag
  • xmanip.htm (examples_2)
• r_free_flags
  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • refinement.htm (creating_r-free_flags_if_not_present_in_the_input_reflection_files__2)
  • refinement.htm (ignoring_test_free_flags_in_refinement_2)
  • refinement.htm (force_anomalous_flag_to_be_equal_to)
  • refinement.htm (force_anomalous_flag_to_be_equal_to_1)
• r_free_flags_fraction
  • refinement.htm (r_free_flags_fraction)
  • autosol.htm (r_free_flags_fraction)
  • autobuild.htm (r_free_flags_fraction)
  • pdbtools.htm (r_free_flags_fraction)
• r_free_flags_lattice_symmetry_max_delta
  • autosol.htm (r_free_flags_lattice_symmetry_max_delta)
  • autobuild.htm (r_free_flags_lattice_symmetry_max_delta)
• r_free_flags_max_free
  • autosol.htm (r_free_flags_max_free)
  • autobuild.htm (r_free_flags_max_free)
• r_free_flags_use_lattice_symmetry
  • autosol.htm (r_free_flags_use_lattice_symmetry)
  • autobuild.htm (r_free_flags_use_lattice_symmetry)
• r_sq_twin
  • xtriage.htm (interpreting_xtriage_output_2)
• r_switch
  • autosol.htm (r_switch)
  • autobuild.htm (r_switch)
• r_unused
  • xtriage.htm (interpreting_xtriage_output_2)
• r_used
  • xtriage.htm (interpreting_xtriage_output_2)
• r_work
  • refinement_examples.htm (examples_2)
• rad_mask_trace
  • find_helices_strands.htm (rad_sep_trace)
• rad_max
  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works__2)
• rad_morph
  • autobuild.htm (morph_rad)
• rad_sep_trace
  • find_helices_strands.htm (ratio_trace_extra)
  • find_helices_strands.htm (rad_sep_trace)
• ramachandran
  • molprobity_tool.htm (authors_2)
  • molprobity_tool.htm (usage_2)
  • phenix_gui.htm (validation_2)
  • validation.htm (overview_2)
  • validation.htm (validation_of_protein_geometry_2)
• ramalyze
  • phenix_gui.htm (validation_2)
• random_scoring
  • autosol.htm (random_scoring)
• random_seed
  • refinement.htm (random_seed_2)
  • refinement.htm (random_seed)
  • refinement.htm (random_seed_1)
  • autobuild.htm (specifying_phenix_refine_parameters_18)
  • autobuild.htm (specifying_phenix_refine_parameters_19)
• randomization
  • autosol.htm (n_random_loop)
  • autobuild.htm (create_one_very_good_rebuilt_model_2)
  • autobuild.htm (include_input_model)
  • autobuild.htm (n_random_loop)
• range_to_keep
  • autosol.htm (max_range_to_keep)
• ratio_b
  • autosol.htm (delta_b_for_auto_correct_aniso)
  • autosol.htm (ratio_b_for_auto_correct_aniso)
• ratio_b_for_auto_correct_aniso
  • autosol.htm (analyzing_and_scaling_the_data_5)
  • autosol.htm (correct_aniso)
  • autosol.htm (delta_b_for_auto_correct_aniso)
  • autosol.htm (ratio_b_for_auto_correct_aniso)
• ratio_out
  • autosol.htm (ratio_out)
  • autosol.htm (require_nat)
  • tutorial_mir.htm (scaling_mir_data_2)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (scaling_mad_data_and_estimating_fa_values_2)
• ratio_trace_extra
  • find_helices_strands.htm (ratio_trace_extra)
• ratmin
  • autosol.htm (ratmin)
• raw_files
  • doc_procedures.htm (generating_current_phenix_html_documents_2)
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
• read_sites
  • autosol.htm (read_sites)
• ready_set
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (add_hydrogens)
  • ready_set.htm
  • ready_set.htm (list_of_all_ready_set_keywords)
  • ready_set.htm (list_of_all_ready_set_keywords_2)
• readyset
  • refinement.htm (hydrogens_in_refinement_2)
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_2)
  • ready_set.htm
  • ready_set.htm (anch1)
  • ready_set.htm (purpose_2)
• real_space_optimize_x_h_orientation
  • refinement.htm (real_space_optimize_x_h_orientation)
• real_space_refinement
  • refinement.htm (use_lattice_symmetry_2)
• real_space_squaring
  • hyss.htm (command_line_options_2)
• real_space_target_weight
  • refinement.htm (real_space_target_weight)
  • ligandfit.htm (real_space_target_weight)
  • find_all_ligands.htm (real_space_target_weight)
• rebuild_after_mr
  • autosol.htm
  • automr.htm (rebuild_after_mr)
  • tutorial_mr.htm (running_the_demo_a2u-globulin-mr_data_with_automr_2)
  • tutorial_mr.htm (summary_of_the_command-line_arguments_2)
• rebuild_chain
  • autobuild.htm (rebuild_chain_list)
  • autobuild.htm (rebuild_res_end_list)
  • autobuild.htm (rebuild_res_start_list)
• rebuild_chain_list
  • autobuild.htm (rebuild_chain_list)
  • autobuild.htm (rebuild_in_place)
  • autobuild.htm (rebuild_near_chain)
  • autobuild.htm (rebuild_near_dist)
  • autobuild.htm (rebuild_near_res)
• rebuild_in_place
  • faqs.htm
  • faqs.htm (autobuild_seems_to_be_taking_a_long_time_what_is_the_usual_time_for_a_run__2)
  • faqs.htm
  • autosol.htm
  • autosol.htm (build_type)
• rebuild_near_chain
  • autobuild.htm (rebuild_near_chain)
  • autobuild.htm (rebuild_near_dist)
  • autobuild.htm (rebuild_near_res)
• rebuild_near_dist
  • autobuild.htm (rebuild_near_chain)
  • autobuild.htm (rebuild_near_dist)
  • autobuild.htm (rebuild_near_res)
• rebuild_near_res
  • autobuild.htm (rebuild_near_chain)
  • autobuild.htm (rebuild_near_dist)
  • autobuild.htm (rebuild_near_res)
• rebuild_res_end_list
  • autobuild.htm (rebuild_chain_list)
  • autobuild.htm (rebuild_in_place)
  • autobuild.htm (rebuild_near_chain)
  • autobuild.htm (rebuild_near_dist)
  • autobuild.htm (rebuild_near_res)
• rebuild_res_start_list
  • autobuild.htm (general_limitations_2)
  • autobuild.htm (rebuild_chain_list)
  • autobuild.htm (rebuild_in_place)
  • autobuild.htm (rebuild_near_chain)
  • autobuild.htm (rebuild_near_dist)
• rebuild_side_chains
  • autobuild.htm (rebuild_side_chains)
• recenter
  • pymol.htm (setting_up_your_view_in_pymol_2)
  • validation.htm (overview_2)
• recommended_resolution
  • autosol.htm (resolution_limits_in_autosol_18)
  • autosol.htm (phase_full_resolution)
• reconstructed_amplitude
  • reflection_statistics.htm (anch1)
• recycle
  • find_helices_strands.htm (recycle)
• recycling
  • hyss.htm (nsf_d2_peak_sca_2)
  • tutorial_mir.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_mad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_sad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
• redo_side_chains
  • autobuild.htm (redo_side_chains)
• reduced
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
  • phaser.htm (poor_or_incomplete_model_2)
  • validation.htm (suggestions_for_improving_models_2)
• reference_coordinates
  • emma.htm (anch1)
• reference_setting
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (standard_laws)
• reference_xray_structure
  • refinement.htm (reference_xray_structure)
• referenced
  • phaser_mr.htm (anch1)
  • phaser_ep.htm (anch1)
• refine
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (command_line_interface_3)
  • running-phenix.htm (command_line_interface_5)
  • phenix-modules.htm (data_analysis_3)
  • phenix-modules.htm (structure_refinement_3)
• refine_adp
  • refinement.htm (refine_adp)
  • refinement.htm (refine_adp_1)
• refine_ap_and_dp
  • refinement.htm (refine_ap_and_dp)
• refine_b
  • autosol.htm (refine_b)
  • autobuild.htm (specifying_phenix_refine_parameters_29)
  • autobuild.htm (refine_b)
• refine_before_rebuild
  • autobuild.htm (refine_before_rebuild)
• refine_eff_file
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild__2)
  • autobuild.htm (twinning_and_autobuild__3)
  • autobuild.htm (specifying_phenix_refine_parameters_3)
  • autobuild.htm (specifying_phenix_refine_parameters_4)
• refine_eff_file_list
  • autosol.htm (refine_eff_file_list)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__3)
  • autobuild.htm (refine_eff_file_list)
• refine_gui
  • refine_gui.htm (launching_2)
• refine_ligand
  • ligandfit.htm (refine_ligand)
  • find_all_ligands.htm (refine_ligand)
• refine_map_coeffs
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• refine_occupancies
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (refine_occupancies)
• refine_rotation
  • refinement.htm (refine_rotation)
• refine_s
  • refinement.htm (refine_s)
• refine_se_occ
  • autosol.htm (refine_se_occ)
  • autobuild.htm (specifying_phenix_refine_parameters_33)
  • autobuild.htm (refine_se_occ)
• refine_sites
  • refinement.htm (refine_sites)
• refine_t
  • refinement.htm (refine_t)
• refine_translation
  • refinement.htm (refine_translation)
• refine_with_ncs
  • autosol.htm (refine_with_ncs)
  • autobuild.htm (specifying_phenix_refine_parameters_13)
  • autobuild.htm (specifying_phenix_refine_parameters_15)
  • autobuild.htm (skip_ncs_in_model_building_and_refinement_2)
  • autobuild.htm (refine_with_ncs)
• refine_x
  • refine_gui.htm (running_phenix_refine_2)
• refine_xyz
  • autobuild.htm (specifying_phenix_refine_parameters_29)
  • autobuild.htm (refine_xyz)
• refinement_examples
  • refinement_examples.htm (quick_facts_2)
  • refinement_examples.htm (run_examples_2)
• refinement_file
  • autobuild.htm (and_optional_files_2)
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_4)
  • autobuild.htm (model)
  • autobuild.htm (refinement_file)
  • autobuild.htm (input_refinement_file)
• refinement_params
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild__2)
  • autobuild.htm (picking_waters_in_autobuild_4)
  • autobuild.htm (specifying_phenix_refine_parameters_3)
• refinement_resolution
  • autosol.htm (resolution_limits_in_autosol_10)
  • autosol.htm (resolution)
  • autosol.htm (refinement_resolution)
  • autobuild.htm (specifying_phenix_refine_parameters_35)
  • autobuild.htm (resolution_limits_in_autobuild_10)
• reflection_file
  • hyss.htm (command_line_options_2)
  • reflection_statistics.htm (anch1)
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• reflection_file_converter
  • running-phenix.htm (command_line_interface_3)
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
  • autosol.htm (data)
  • autosol.htm (group_labels_list)
  • reflection_file_tools.htm
• reflection_statistics
  • xtriage.htm (how_xtriage_works_2)
  • hyss.htm
  • hyss.htm (phenix_reflection_statistics)
  • hyss.htm (phenix_reflection_statistics_2)
  • reflection_statistics.htm (anch1)
• refmac
  • create_maps.htm (guidelines_for_use_2)
• regularization
  • pdbtools.htm (anch1)
• regularize
  • pdbtools.htm (action)
• regularize_ncycles
  • refinement.htm (regularize_ncycles)
• reindex
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (action)
• reindexing
  • running-phenix.htm (command_line_interface_3)
  • xtriage.htm (low_resolution)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (action)
• rejection
  • autosol.htm (ratio_out)
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (what_to_do_next_2)
  • tutorial_sad.htm (what_to_do_next_2)
• relative_length_tolerance
  • explore_metric_symmetry.htm (keywords_2)
• remove_aniso
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• resolution_factor
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  • phenix-environment.htm (setting_up_your_environment_2)
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  • faqs.htm (what_do_i_do_if_autobuild_says_tried_resolve_extra_huge__but_not_ok__2)
  • autosol.htm (resolve_command_list)
  • autosol.htm (solve_command_list)
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  • tutorial_ligandfit.htm (what_to_do_next_2)
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  • autobuild.htm
  • autobuild.htm (specifying_resolve_resolve_pattern_parameters)
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  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_gui__5)
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• resolve_pattern_command_list
  • autobuild.htm (resolve_pattern_command_list)
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  • autobuild.htm (resolve_size)
  • ligandfit.htm (resolve_size)
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  • tutorial_build.htm (model-building_with_resolve_2)
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  • tutorial_mir.htm (reading_the_log_files_for_your_autosol_run_file_2)
  • tutorial_mr.htm (reading_the_log_files_for_your_automr_run_file_2)
  • tutorial_ligandfit.htm (reading_the_log_files_for_your_ligandfit_run_file_2)
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  • autobuild.htm (restart_cycle_after_morph)
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• restraint_group
  • refinement.htm (using_ncs_restraints_in_refinement_2)
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  • refinement.htm (use_lattice_symmetry_2)
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• rho_cut_min
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• rhombohedral
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  • ligandfit.htm (specific_limitations_and_problems_9)
  • automr.htm (specific_limitations_and_problems_9)
  • running-wizards.htm (specific_limitations_and_problems__7)
• richardson
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  • autobuild.htm (richardson_rotamers)
  • molprobity_tool.htm (authors_2)
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  • refinement.htm (refinement_scenarios_2)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (strategy)
• rigid_body_groups_selections
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
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  • refinement.htm (refinement_of_coordinates_2)
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• rigid_bond_test
  • refinement.htm (rigid_bond_test)
• ring
  • ligandfit.htm (specific_limitations_and_problems_6)
  • xtriage.htm (how_xtriage_works_2)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage_gui.htm
  • xtriage_gui.htm (data_quality_analyses_2)
• rms_random_frag
  • autosol.htm (rms_random_frag)
  • autobuild.htm (rms_random_frag)
• rms_random_loop
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  • autosol.htm (rms_random_loop)
  • autosol.htm (thorough_loop_fit)
  • autobuild.htm (rms_random_loop)
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• rmsd_cutoff_for_gradient_filtering
  • refinement.htm (rmsd_cutoff_for_gradient_filtering)
• rmsd_max
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• rmsd_max_angles
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• rmsd_max_bonds
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• rotomer
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  • examples.htm (what_sample_data_are_available_to_run_automatically__2)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_2)
• run_finite_differences_test
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• runtime
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  • autobuild.htm (make_a_sa-omit_map_around_atoms_in_target_pdb_2)
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  • autobuild.htm (make_a_sa-omit_map_around_residues_3_and_4_in_chain_a_of_coords_pdb_2)
• sca_hyss
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  • tutorial_mad.htm (the_autosol_summary_dat_summary_file_2)
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  • refinement.htm (modifying_the_initial_model_before_refinement_starts_2)
  • refinement.htm (scale_adp)
  • pdbtools.htm (scale_adp)
• scale_k1
  • refinement.htm (reflection_output_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
  • refinement.htm (use_f_model_scaled)
• scale_max
  • refinement.htm (scale_max)
• scale_min
  • refinement.htm (scale_min)
• scale_molp_score
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• scale_weight
  • xmanip.htm (command_line_interface_2)
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  • xmanip.htm (scale_weight_1)
• scalepack_merge
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• scalepack_no_merge_original_index
  • tutorial_mir.htm (reading_the_datafiles__2)
• scatterers
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (relevant_reading_2)
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  • hyss.htm (hyss_overview_2)
• scattering_table
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_2)
  • refinement.htm (scattering_factors_2)
  • refinement.htm (scattering_table)
  • refinement.htm (scattering_table_1)
  • pdbtools.htm (anch1)
• scattering_type
  • refinement.htm (scattering_type)
• scope
  • refinement.htm (f_and_f_refinement_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (list_of_all_refinement_keywords_2)
  • refinement.htm (space_group)
  • refinement.htm (file_name)
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  • autosol.htm (score_individual_sd_list)
• score_individual_scale_list
  • autosol.htm (score_individual_offset_list)
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  • autosol.htm (score_individual_sd_list)
• score_individual_sd_list
  • autosol.htm (score_individual_offset_list)
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• score_overall_offset
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• score_overall_sd
  • autosol.htm (score_overall_sd)
• score_type_list
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (score_type_list)
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  • autosol.htm (overall_score_method)
• score_weight_list
  • autosol.htm (score_weight_list)
• screw
  • reflection_file_editor.htm (notes_on_usage_2)
  • tutorial_mir.htm (what_to_do_next_2)
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• sculptor
  • phenix_gui.htm (model_tools_2)
• sd_of_random_solution_scores
  • autosol.htm (scoring_of_heavy-atom_solutions_4)
• search_center
  • ligandfit.htm (ligand_near_chain)
  • ligandfit.htm (ligand_near_res)
  • ligandfit.htm (search_center)
  • find_all_ligands.htm (ligand_near_chain)
  • find_all_ligands.htm (ligand_near_res)
• search_dist
  • ligandfit.htm (local_search)
  • ligandfit.htm (search_dist)
  • find_all_ligands.htm (local_search)
  • find_all_ligands.htm (search_dist)
• search_model
  • automr.htm (what_the_automr_wizard_needs_to_run_5)
• search_parameters
  • ligandfit.htm (cif_def_file_list)
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• search_target
  • ligandfit.htm (fit_phi_range)
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• searches
  • autosol.htm (mad_ha_add_list)
  • automr.htm (specific_limitations_and_problems_5)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • map_to_object.htm (how_phenix_map_to_object_works__2)
  • find_helices_strands.htm (target_p_ratio)
• second_and_before_last
  • refinement.htm (refinement_of_coordinates_2)
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• secondary_map_and_map_cc_filter
  • refinement.htm (water_picking_2)
  • refinement.htm (use_kick_maps)
• seeding
  • find_helices_strands.htm (pdb_in)
• selection_criteria_rot
  • automr.htm (selection_criteria_rot)
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • automr.htm (selection_criteria_rot_value)
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • superpose_pdbs.htm (standard_run_of_superpose_pdbs__2)
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  • superpose_pdbs.htm (selection_fixed)
  • superpose_pdbs.htm (selection_moving)
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  • superpose_pdbs.htm (standard_run_of_superpose_pdbs__2)
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• selenomethionine
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  • autobuild.htm (semet)
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  • autobuild.htm (semi_acceptable_r)
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• seq_file
  • faqs.htm
  • faqs.htm
  • faqs.htm
  • autosol.htm (setting_up_inputs_5)
  • autosol.htm (how_to_run_the_autosol_wizard_5)
• seq_from_seqres_records
  • autosol.htm (seq_file)
  • autobuild.htm (seq_file)
• seqres
  • autosol.htm (seq_file)
  • autobuild.htm (seq_file)
• sequence
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
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  • phenix-modules.htm (literature_2)
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  • refinement.htm (using_ncs_restraints_in_refinement_2)
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  • refinement.htm (serial_format)
• set_b
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (task_1)
• set_b_iso
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_2)
  • refinement.htm (set_b_iso)
  • pdbtools.htm (anch1)
  • pdbtools.htm (set_b_iso)
• set_cc_to_zero_if_n_grid_points_less_than
  • refinement.htm (set_cc_to_zero_if_n_grid_points_less_than)
• set_chemical_element_simple_if_necessary
  • refinement.htm (set_chemical_element_simple_if_necessary)
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  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
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  • find_helices_strands.htm (target_p_ratio)
  • find_helices_strands.htm (optimize)
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  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_2)
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  • elbow.htm (output_2)
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  • refinement.htm (temperature_cap_factor)
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  • refinement.htm (temperature_degrees_of_freedom)
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  • autosol.htm (test_correct_aniso)
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  • autosol.htm (test_mask_type)
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  • autosol.htm (quick)
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  • find_ncs.htm (ncs_thorough)
  • find_helices_strands.htm (target_p_ratio)
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  • refinement.htm (time_step_factor)
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  • refinement.htm (time_step_pico_seconds)
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  • phenix-modules.htm (structure_refinement_3)
  • phenix-modules.htm (literature_2)
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  • refinement.htm (current_limitations_2)
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  • refinement.htm
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
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  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
• to_inverse_hand
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
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  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
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  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
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  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
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  • refinement.htm (definition_of_custom_bonds_and_angles_2)
  • refinement.htm (lattice_symmetry_max_delta_2)
  • simple_ncs_from_pdb.htm (how_simple_ncs_from_pdb_works__5)
  • find_helices_strands.htm (dist_ca_tol_max)
  • find_helices_strands.htm (dist_ca_start)
• tolerances
  • find_helices_strands.htm (trace_ratio_long)
  • explore_metric_symmetry.htm (keywords_2)
  • tutorial_twin.htm (examples_2)
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  • ligandfit.htm (top_output_dir)
  • automr.htm (top_output_dir)
  • find_all_ligands.htm (top_output_dir)
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  • refinement.htm (simulated_annealing_torsion)
  • ligandfit.htm (conformers)
  • find_all_ligands.htm (conformers)
  • validation.htm (geometry_restraints_outliers_2)
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  • refinement.htm (torsion_angles)
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  • autobuild.htm (min_cc_res_rebuild)
  • autobuild.htm (replace_existing)
  • autobuild.htm (touch_up)
  • autobuild.htm (touch_up_extra_residues)
• touch_up_extra_residues
  • autobuild.htm (touch_up_extra_residues)
• tough
  • phenix_gui.htm (phasing_2)
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  • autosol.htm (trace_as_lig)
  • autobuild.htm (trace_as_lig)
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  • autosol.htm (trace_chain)
  • autosol.htm (trace_chain_score)
  • find_helices_strands.htm
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps_)
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
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  • autosol.htm (trace_chain_score)
• trace_ratio_long
  • find_helices_strands.htm (trace_ratio_long)
• track_libs
  • autobuild.htm (track_libs)
• trailing
  • reflection_file_editor.htm (notes_on_usage_2)
• trajectory_directory
  • refinement.htm (trajectory_directory)
• tran_orth
  • simple_ncs_from_pdb.htm (standard_run_of_simple_ncs_from_pdb__6)
• transformations
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__4)
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  • refinement.htm (modifying_the_initial_model_before_refinement_starts_2)
  • refinement.htm (translate)
  • pdbtools.htm (translate)
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  • refinement.htm (translate_cns_dna_rna_residue_names)
  • pdbtools.htm (translate_cns_dna_rna_residue_names)
• translation
  • running-phenix.htm (tasks_and_strategies_3)
  • phenix-modules.htm (literature_2)
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_2)
  • refinement.htm (refine_rotation)
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  • phenix_gui.htm (model_tools_2)
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  • autosol.htm (scoring_of_heavy-atom_solutions_2)
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  • autobuild.htm
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  • autosol.htm (truncate_ha_sites_in_resolve)
  • autobuild.htm (truncate_density_at_heavy-atom_sites_2)
  • autobuild.htm (input_ha_file)
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  • refinement.htm (truncate_to_polyala)
  • pdbtools.htm (truncate_to_polyala)
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  • phaser.htm
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  • phenix-modules.htm (data_analysis_3)
  • faqs.htm
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild_)
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  • refinement.htm (refinement_using_twinned_data_2)
• twin_law
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  • refinement.htm (refinement_using_twinned_data_2)
  • refinement.htm (twin_law)
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  • autobuild.htm (specifying_phenix_refine_parameters_3)
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  • refinement.htm (twin_target)
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  • phenix-modules.htm (data_analysis_3)
  • refinement.htm (refinement_using_twinned_data_2)
  • tutorial_twin.htm (a_quick_model_based_twinning_analysis_2)
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  • refinement.htm (twin_target)
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  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (n_bins)
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  • phenix-modules.htm (literature_2)
  • refinement.htm
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  • refinement.htm (refinement_using_twinned_data)
  • refinement.htm (refinement_using_twinned_data_2)
• twinning_parameters
  • xtriage.htm (action_2)
• twinning_with_ncs
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (sigma_inflation)
• two_adp_groups_per_residue
  • refinement.htm
  • refinement.htm (group_adp_refinement_mode)
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  • autobuild.htm (twinning_and_autobuild__4)
  • autobuild.htm (two_fofc_in_rebuild)
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  • automr.htm (two_fofc_in_rebuild)
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  • refinement.htm (twofofc)
  • tutorial_twin.htm (map_inspection_2)
• u_base
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  • refinement.htm (u_base_1)
  • pdbtools.htm (u_base)
• u_cif
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• u_overall
  • refinement.htm (reflection_output_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
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  • tutorial_mir.htm (how_do_i_know_if_i_have_a_good_solution__2)
  • tutorial_mad.htm (how_do_i_know_if_i_have_a_good_solution__2)
• uncertainty
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (score_individual_offset_list)
  • autosol.htm (score_individual_scale_list)
  • autosol.htm (score_individual_sd_list)
  • autosol.htm (score_overall_sd)
• understanding
  • phenix_gui.htm (modules_2)
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  • autosol.htm (max_extra_unique_solutions)
• unit cell
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  • faqs.htm
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  • faqs.htm
  • faqs.htm
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  • autosol.htm (specific_limitations_and_problems_4)
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  • autobuild.htm (general_limitations_3)
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  • autosol.htm (datafile_formats_in_autosol_4)
  • hyss.htm (hyss_examples_2)
  • tutorial_mir.htm (reading_the_datafiles__2)
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  • multi_crystal_average.htm (sharpen)
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  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • pdbtools.htm (use_asu_masks)
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  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (use_contact_order)
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  • refinement.htm (default_refinement_with_user_specified_x-ray_target_function_2)
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  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (use_fixed_center_of_mass)
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  • refinement.htm (use_form_factor_weights)
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  • refinement.htm (use_geometry_restratints)
• use_hydrogens
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  • xmanip.htm (command_line_interface_2)
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  • refinement.htm (use_kick_maps)
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  • refinement.htm (use_lattice_symmetry)
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  • refinement.htm (use_map)
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  • autosol.htm (use_met_in_align)
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  • autobuild.htm (specifying_phenix_refine_parameters_27)
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  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__7)
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  • multi_crystal_average.htm (write_ncs_domain_pdb)
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  • map_to_object.htm
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (use_moving_center_of_mass)
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  • get_cc_mtz_pdb.htm (use_only_refl_present_in_mtz)
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  • autosol.htm (use_perfect)
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  • refinement.htm (use_u_local_only)
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  • xmanip.htm (command_line_interface_2)
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  • xmanip.htm (standard_operators)
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  • xmanip.htm (user_supplied_law)
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  • xmanip.htm (standard_operators)
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  • xmanip.htm (command_line_interface_2)
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• utilities
  • doc_procedures.htm (generating_current_phenix_html_documents_2)
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  • coot.htm (anch1)
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  • validation.htm (running_validation_2)
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  • phenix_gui.htm (validation_2)
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  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
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  • pdbtools.htm (vdw_1_4_factor)
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  • refinement.htm (lattice_symmetry_max_delta_2)
  • autosol.htm (hyss_n_patterson_vectors)
  • xtriage.htm (interpreting_xtriage_output_2)
  • explore_metric_symmetry.htm (purpose_2)
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  • refinement.htm (random_seed_2)
• velocity_scaling
  • refinement.htm (velocity_scaling)
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  • phaser_mr.htm (additional_parameters_2)
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  • faqs.htm
  • refinement.htm (symmetry_safety_check)
  • refine_gui.htm (creating_restraints_2)
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  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • autosol.htm (output_files_from_autosol_6)
  • autobuild.htm (output_files_from_autobuild_3)
  • ligandfit.htm (output_files_from_ligandfit_6)
  • automr.htm (output_files_from_automr_5)
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  • refinement.htm
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  • refinement.htm
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  • refinement.htm (water_picking_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (scattering_type)
  • refinement.htm (b_iso_min)
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  • refinement.htm (f_and_f_refinement_2)
  • autosol.htm (setting_up_inputs_8)
  • autosol.htm (finding_heavy-atom_anomalously-scattering_atom_sites_3)
  • autosol.htm (running_from_a_parameters_file_2)
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  • autosol.htm (wavelength_list)
• wavelength_name
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • autosol.htm (wavelength_name)
  • autosol.htm (wavelength_name_1)
  • tutorial_mir.htm (summary_of_the_command-line_arguments_2)
  • tutorial_mad.htm (summary_of_the_command-line_arguments_2)
• wavelength_name_list
  • autosol.htm (wavelength_name_list)
• wavelengths
  • autosol.htm (atom_type)
  • autosol.htm (lambda)
  • autosol.htm (f_prime)
  • autosol.htm (f_double_prime)
  • autosol.htm (wavelength_name)
• wc_scale
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm
• weight
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm (optimizing_target_weights_2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (random_seed_2)
  • refinement.htm (definition_of_custom_bonds_and_angles_2)
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  • automr.htm (weight_list)
• weight_ncs
  • multi_crystal_average.htm (weight_ncs)
• weight_seq_list
  • automr.htm (weight_seq_list)
• weights
  • phenix-modules.htm (structure_refinement_3)
  • faqs.htm (why_doesnt_coot_recognize_my_mtz_file_from_autobuild___2)
  • refinement.htm
  • refinement.htm (optimizing_target_weights)
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  • refinement.htm (cif_modifications_and_links_2)
• wiki
  • phaser_mr.htm (anch1)
  • phaser_ep.htm (anch1)
• wildcard
  • refinement.htm (atom_selection_examples_2)
• wilson_b_weight
  • refinement.htm (wilson_b_weight)
• wilson_b_weight_auto
  • refinement.htm (wilson_b_weight_auto)
• wing_cutoff
  • refinement.htm (wing_cutoff)
  • refinement.htm (wing_cutoff_1)
  • pdbtools.htm (wing_cutoff)
• wnc_scale
  • refinement.htm (wnc_scale)
• wnu_scale
  • refinement.htm (wnu_scale)
• workbench
  • what-is-phenix.htm (anch1_3)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • elbow.htm
  • elbow.htm (anch1)
  • elbow.htm (literature_2)
• worried
  • create_maps.htm (guidelines_for_use_2)
• worst_percent_res_rebuild
  • autobuild.htm (touch_up_a_model__2)
  • autobuild.htm (min_cc_res_rebuild)
  • autobuild.htm (touch_up)
  • autobuild.htm (worst_percent_res_rebuild)
• write_def_file
  • refinement.htm (suppressing_the_output_of_certain_files_2)
  • refinement.htm (write_def_file)
  • autobuild.htm (specifying_phenix_refine_parameters_38)
• write_eff_file
  • refinement.htm (suppressing_the_output_of_certain_files_2)
  • refinement.htm (write_eff_file)
  • autobuild.htm (specifying_phenix_refine_parameters_38)
• write_geo_file
  • refinement.htm (suppressing_the_output_of_certain_files_2)
  • refinement.htm (write_geo_file)
  • autobuild.htm (specifying_phenix_refine_parameters_38)
• write_map_coefficients
  • refinement.htm (suppressing_the_output_of_certain_files_2)
  • refinement.htm (write_map_coefficients)
  • autobuild.htm (specifying_phenix_refine_parameters_38)
• write_maps
  • refinement.htm (suppressing_the_output_of_certain_files_2)
  • refinement.htm (write_maps)
  • autobuild.htm (specifying_phenix_refine_parameters_38)
• write_modified
  • refinement.htm (new_id)
  • pdbtools.htm (new_id)
• write_mtz_amplitudes
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• write_ncs_domain_pdb
  • refinement.htm (write_ncs_domain_pdb)
  • simple_ncs_from_pdb.htm (write_ncs_domain_pdb)
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__7)
  • multi_crystal_average.htm
  • multi_crystal_average.htm (use_model_mask)
• write_out
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (write_out)
• write_run_directory_to_file
  • autosol.htm (write_run_directory_to_file)
  • autobuild.htm (write_run_directory_to_file)
  • ligandfit.htm (write_run_directory_to_file)
  • automr.htm (write_run_directory_to_file)
  • find_all_ligands.htm (write_run_directory_to_file)
• wxc_scale
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (wxc_scale)
• wxu_scale
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__2)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_2)
  • refinement.htm (wxu_scale)
• xds_ascii
  • hyss.htm (hyss_examples_2)
• xh_bond_distance_deviation_limit
  • refinement.htm (xh_bond_distance_deviation_limit)
• xplor
  • running-phenix.htm (command_line_interface_4)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_2)
  • refinement.htm (map_format)
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • pymol.htm (useful_pymol_commands_2)
• xray_data
  • refinement.htm (running_phenix_refine_2)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_2)
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_2)
  • refinement.htm (creating_r-free_flags_if_not_present_in_the_input_reflection_files__2)
  • refinement.htm (setting_the_resolution_range_for_the_refinement_2)
• xray_weight_factor
  • refinement.htm (xray_weight_factor)
• xtriage_gui
  • xtriage_gui.htm (configuration_2)
• yeates
  • phenix-modules.htm (literature_2)
  • xtriage.htm (interpreting_xtriage_output_2)
• z_score
  • automr.htm (selection_criteria_rot)
  • xtriage.htm (interpreting_xtriage_output_2)
• zn_selection
  • refinement.htm (definition_of_custom_bonds_and_angles_2)
• zone
  • refinement.htm (refinement_of_coordinates_2)
  • refinement.htm (min_number_of_reflections)
  • refinement.htm (max_low_high_res_limit)
• zone_exponent
  • refinement.htm (zone_exponent)