Index for PHENIX web site

• _extra_huge
  • autosol.htm (specific_limitations_and_problems_3)
  • autosol.htm (resolve_size)
  • autobuild.htm (specific_limitations_and_problems_2)
  • autobuild.htm (resolve_size)
  • ligandfit.htm (specific_limitations_and_problems_7)
• _giant
  • autosol.htm (specific_limitations_and_problems_3)
  • autosol.htm (resolve_size)
  • autobuild.htm (specific_limitations_and_problems_2)
  • autobuild.htm (resolve_size)
  • ligandfit.htm (specific_limitations_and_problems_7)
• _huge
  • autosol.htm (specific_limitations_and_problems_3)
  • autosol.htm (resolve_size)
  • autobuild.htm (specific_limitations_and_problems_2)
  • autobuild.htm (resolve_size)
  • ligandfit.htm (specific_limitations_and_problems_7)
• abnormalities
  • xtriage.htm (interpreting_xtriage_output_17)
  • xtriage.htm (interpreting_xtriage_output_23)
• absence
  • pdbtools.htm (anch1_5)
• absolute_angle_tolerance
  • explore_metric_symmetry.htm (keywords_3)
  • explore_metric_symmetry.htm (keywords_9)
• 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_4)
  • tutorial_mad.htm (model-building_with_resolve_4)
  • tutorial_sad.htm (model-building_with_resolve_4)
• acentric
  • xtriage.htm (interpreting_xtriage_output_20)
  • xtriage.htm (interpreting_xtriage_output_35)
  • xtriage.htm (interpreting_xtriage_output_38)
  • xtriage.htm (interpreting_xtriage_output_39)
  • xtriage.htm (interpreting_xtriage_output_42)
• add_h
  • pdbtools.htm (anch1_28)
• add_sidechains
  • autosol.htm (add_sidechains)
• adp_restraints
  • refinement.htm (eps)
• after_autosol
  • autosol.htm (input_seq_file)
  • autobuild.htm (run_autobuild_automatically_after_autosol_2)
  • autobuild.htm (after_autosol)
  • autobuild.htm (input_map_file)
  • autobuild.htm (input_refinement_file)
• algebraic
  • refinement.htm (refinement_using_twinned_data_6)
  • refinement.htm (mode_4)
  • 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__5)
• alignment_style
  • superpose_pdbs.htm (alignment_style)
• aligns
  • tutorial_mir.htm
• all_plausible_sg_list
  • automr.htm (all_plausible_sg_list)
  • automr.htm (use_all_plausible_sg)
  • tutorial_mr.htm (running_phaser_molecular_replacement_4)
• allow_negative_residues
  • autobuild.htm (allow_negative_residues)
• alpha_beta
  • refinement.htm (b23)
• alternate_nonbonded_off_on
  • pdbtools.htm (alternate_nonbonded_off_on)
• ambiguity
  • hyss.htm (nsf_d2_peak_sca_7)
  • emma.htm (anch1_4)
• angle_ideal
  • refinement.htm (definition_of_custom_bonds_and_angles_3)
  • 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_5)
  • 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_3)
  • refinement.htm (anisotropic_scaling)
• anisotropy
  • refinement.htm (refinement_using_twinned_data_5)
  • refinement.htm (relevant_reading_3)
  • autosol.htm (analyzing_and_scaling_the_data_4)
  • autosol.htm (analyzing_and_scaling_the_data_5)
  • autosol.htm (analyzing_and_scaling_the_data_6)
• anisotropy_min
  • refinement.htm (anisotropy_min)
• anomalous
  • phenix-modules.htm (literature_2)
  • faqs.htm (can_phenix_do_mrsad__3)
  • faqs.htm (can_phenix_do_mrsad__4)
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__3)
  • faqs.htm (how_do_i_know_what_my_choices_of_labels_are_for_my_data_file__4)
• anomalous_difference_map
  • refinement.htm (calc_factor_2)
• anomalous_scatterers
  • refinement.htm (f_and_f_refinement_3)
  • refinement.htm (f_and_f_refinement_5)
  • refinement.htm (one_occupancy_group_per_residue)
• anoonly
  • autosol.htm (inano_list)
  • autosol.htm (inano)
  • autosol.htm (inano_1)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_7)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_10)
• antiparallel
  • tutorial_mir.htm (how_do_i_know_if_i_have_a_good_solution__3)
  • tutorial_mad.htm (how_do_i_know_if_i_have_a_good_solution__3)
  • tutorial_sad.htm (how_do_i_know_if_i_have_a_good_solution__3)
• apply_b_factor_sharpening
  • refinement.htm (apply_b_factor_sharpening)
• apply_back_trace_of_b_cart
  • refinement.htm (apply_back_trace_of_b_cart)
• apply_cif_link
  • refinement.htm (cif_modifications_and_links_6)
  • refinement.htm (cif_modifications_and_links_8)
  • refinement.htm (residue_selection)
  • pdbtools.htm (residue_selection)
• apply_cif_modification
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (cif_modifications_and_links_4)
  • refinement.htm (cif_modifications_and_links_8)
  • refinement.htm (translate_cns_dna_rna_residue_names)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__4)
• 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_4)
  • refinement.htm (apply_sigma_scaling)
• apply_volume_scaling
  • refinement.htm (electron_density_maps_4)
  • refinement.htm (apply_volume_scaling)
• approximations
  • refinement.htm (fft_vs_direct)
• assessment
  • running-phenix.htm (command_line_interface_3)
  • xtriage.htm
  • xtriage.htm (literature_2)
  • tutorial_mir.htm (running_phenix_xtriage_3)
  • tutorial_rebuild.htm (running_phenix_xtriage_3)
• asu_contents
  • xtriage.htm (xtriage_keywords_in_detail_3)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (expert_level)
• asuset
  • autosol.htm (specific_limitations_and_problems_6)
  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_8)
  • automr.htm (specific_limitations_and_problems_6)
  • running-wizards.htm (specific_limitations_and_problems__8)
• asymmetric
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • refinement.htm (use_lattice_symmetry_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_16)
  • autosol.htm (specific_limitations_and_problems_3)
  • autobuild.htm (specific_limitations_and_problems_2)
• atom_id
  • refinement.htm (cif_modifications_and_links_4)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__3)
• atom_selection
  • refinement.htm (occupancy_refinement_3)
  • refinement.htm (electron_density_maps_4)
  • refinement.htm (electron_density_maps_5)
  • refinement.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_3)
• atomtype
  • tutorial_sad.htm (final_phasing_with_phaser_2)
• auto_mr
  • phaser.htm (general_strategy_for_automated_molecular_replacement_4)
  • phaser.htm (how_to_select_peaks_2)
• autobuild
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (command_line_interface_9)
  • 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_debug
  • automr.htm (autobuild_debug)
• autobuild_facts
  • autobuild.htm (output_files_from_autobuild_3)
• autobuild_i_ran_seed
  • automr.htm (autobuild_i_ran_seed)
• autobuild_include_input_model
  • automr.htm (autobuild_include_input_model)
• autobuild_input_labels
  • faqs.htm
  • automr.htm (autobuild_input_labels)
• autobuild_input_list_add
  • automr.htm (passing_any_commands_to_autobuild_3)
  • automr.htm (autobuild_input_list_add)
• autobuild_input_refinement_file
  • automr.htm (specifying_a_refinement_file_for_autobuild_3)
  • automr.htm (autobuild_input_refinement_file)
• autobuild_input_refinement_labels
  • automr.htm (specifying_a_refinement_file_for_autobuild_3)
  • automr.htm (autobuild_input_refinement_labels)
• autobuild_lores
  • tutorial_rebuild.htm (what_parameters_did_i_use__2)
  • tutorial_build.htm (what_parameters_did_i_use__2)
• autobuild_n_cycle_build_max
  • automr.htm (autobuild_n_cycle_build_max)
• autobuild_n_cycle_build_min
  • automr.htm (autobuild_n_cycle_build_min)
• autobuild_n_cycle_rebuild_max
  • automr.htm (autobuild_n_cycle_rebuild_max)
• autobuild_n_cycle_rebuild_min
  • automr.htm (autobuild_n_cycle_rebuild_min)
• autobuild_nbatch
  • automr.htm (autobuild_nbatch)
• autobuild_nproc
  • automr.htm (autobuild_nproc)
• autobuild_rebuild_in_place
  • automr.htm (autobuild_rebuild_in_place)
• autobuild_refine
  • automr.htm (passing_any_commands_to_autobuild_3)
  • automr.htm (autobuild_input_list_add)
• autobuild_resolution
  • automr.htm (passing_any_commands_to_autobuild_3)
• autobuild_resolve_command_list
  • automr.htm (autobuild_resolve_command_list)
• autobuild_resolve_pattern_command_list
  • automr.htm (autobuild_resolve_pattern_command_list)
• autobuild_semet
  • automr.htm (passing_any_commands_to_autobuild_3)
  • automr.htm (autobuild_input_list_add)
• autobuild_start_chains_list
  • automr.htm (autobuild_start_chains_list)
• autobuild_summary
  • autobuild.htm (output_files_from_autobuild_3)
  • autobuild.htm (output_files_from_autobuild_4)
  • tutorial_rebuild.htm
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file)
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
• autobuild_thorough_denmod
  • automr.htm (autobuild_thorough_denmod)
• autobuild_two_fofc_in_rebuild
  • automr.htm (autobuild_two_fofc_in_rebuild)
• autobuild_warnings
  • autobuild.htm (output_files_from_autobuild_3)
• automatic_randomization_if_all_equal
  • refinement.htm (automatic_randomization_if_all_equal)
• automr
  • running-phenix.htm (command_line_interface_9)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • faqs.htm
  • faqs.htm (can_phenix_do_mrsad__3)
• automr_auto_mr
  • tutorial_mr.htm (running_phaser_molecular_replacement_3)
• 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)
• autosol
  • running-phenix.htm (command_line_interface_9)
  • 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_3)
  • tutorial_mad.htm (guessing_cell_contents_3)
  • tutorial_sad.htm (guessing_cell_contents_3)
• autosol_hires
  • tutorial_sad.htm (what_parameters_did_i_use__2)
• autosol_lores
  • 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
  • refinement.htm (water_picking_9)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__7)
  • 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_7)
  • refinement.htm (b_cart)
  • xtriage.htm (interpreting_xtriage_output_11)
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (k_overall)
• b_either
  • refinement.htm (water_picking_9)
• b_factor_weight
  • refinement.htm (b_factor_weight)
  • refinement.htm (b_factor_weight_1)
• b_individual
  • refinement.htm
• b_iso
  • refinement.htm (water_picking_8)
  • refinement.htm (water_picking_9)
  • refinement.htm (b_iso)
  • xtriage.htm (b_iso)
  • xmanip.htm (command_line_interface_2)
• b_iso_max
  • refinement.htm (water_picking_8)
  • refinement.htm (b_iso_max)
  • refinement.htm (b_iso_max_1)
  • refinement.htm (b_iso_max_2)
• b_iso_min
  • refinement.htm (water_picking_8)
  • 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_5)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
  • refinement.htm (developers_tools_7)
  • 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_14)
• background
  • autosol.htm (background)
  • autosol.htm (run_command)
  • autobuild.htm (background)
  • autobuild.htm (run_command)
  • ligandfit.htm (background)
• background_map
  • autobuild.htm (background_map)
• backslash
  • refinement.htm (atom_selection_examples_6)
  • tutorial_mr.htm (running_the_demo_a2u-globulin-mr_data_with_automr_6)
  • tutorial_rebuild.htm (running_the_demo_a2u-globulin-rebuild_data_with_autobuild_6)
  • tutorial_build.htm (running_the_demo_p9-build_data_with_autobuild_6)
  • tutorial_mad.htm (running_the_demo_gene-5_data_with_autosol_7)
• 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_10)
• bayes
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (scoring_of_heavy-atom_solutions_5)
  • autosol.htm (scoring_of_heavy-atom_solutions_6)
  • autosol.htm (overall_score_method)
  • autosol.htm (score_type_list)
• bayesian
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_5)
  • autosol.htm (scoring_of_heavy-atom_solutions_14)
  • autosol.htm (mir_dataset_5)
  • autosol.htm (literature_3)
• 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)
• beta
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___3)
  • autosol.htm (cell)
  • autobuild.htm (cell)
  • ligandfit.htm (cell)
  • automr.htm (automr_searching_for_2_components_3)
• bf_atoms_absent
  • refinement.htm (bf_atoms_absent)
• bfgs
  • refinement.htm (relevant_reading_3)
• bijvoet
  • refinement.htm
  • autosol.htm (input_refinement_file)
  • autobuild.htm (input_refinement_file)
  • automr.htm (input_refinement_file)
  • xtriage.htm (interpreting_xtriage_output_25)
• 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_3)
  • elbow.htm (novice_options__244)
  • reel.htm (input_3)
• 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 (boundary_background_map)
  • autobuild.htm (offset_boundary)
• 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_42)
  • xtriage.htm (interpreting_xtriage_output_45)
  • xtriage.htm (interpreting_xtriage_output_52)
  • xtriage.htm (interpreting_xtriage_output_53)
• bsharp
  • refinement.htm (apply_b_factor_sharpening)
• build
  • faqs.htm (what_sample_data_are_available_to_run_automatically__4)
  • faqs.htm
  • faqs.htm
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___3)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
• build_ias_types
  • refinement.htm (build_ias_types)
• build_model
  • autobuild.htm (build_outside)
  • autobuild.htm (connect)
• build_only
  • refinement.htm (build_only)
• build_outside
  • autobuild.htm (build_outside)
  • tutorial_build.htm (model-building_with_resolve_12)
• build_type
  • autosol.htm (build_type)
  • autosol.htm (n_cycle_build)
  • autobuild.htm (build_type)
  • autobuild.htm (n_cycle_build)
  • 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_3)
  • refinement.htm (bulk_solvent)
• bulk_solvent_and_scale
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_3)
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_4)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
  • refinement.htm (bulk_solvent_and_scale)
  • refinement.htm (bulk_solvent_and_scale_1)
• calc
  • refinement.htm (method)
• calc_factor
  • refinement.htm (electron_density_maps_4)
  • refinement.htm (calc_factor)
  • refinement.htm (calc_factor_1)
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  • autobuild.htm (make_an_iterative-build_omit_map_around_atoms_in_target_pdb_2)
  • autobuild.htm (make_a_sa-omit_map_around_residues_3_and_4_in_chain_a_of_coords_pdb_2)
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  • elbow.htm
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  • molprobity_tool.htm (authors_2)
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  • autosol.htm (mad_dataset_3)
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  • faqs.htm (what_is_an_r-free_flags_mismatch__4)
  • autosol.htm
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  • autosol.htm (analyzing_and_scaling_the_data_5)
  • autosol.htm (correct_aniso)
  • autosol.htm (delta_b_for_auto_correct_aniso)
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  • ligandfit.htm (delta_phi_ligand)
• delta_range_2p_max
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• delta_slack
  • refinement.htm (definition_of_custom_bonds_and_angles_6)
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• denmod
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  • tutorial_mad.htm (the_autosol_summary_dat_summary_file_2)
• density modification
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  • running-phenix.htm (tasks_and_strategies_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
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• deriv_hyss_consensus_model
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• descriptor
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  • autosol.htm (desired_coverage)
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  • refinement.htm (twin_law)
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• dfmodel
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  • refinement.htm (map_type)
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• dihedral_angle_deviations_from_ideal
  • refinement.htm (dihedral_angle_deviations_from_ideal)
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• dihedrals
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  • refinement.htm (dihedrals)
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• direct methods
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  • tutorial_mir.htm (running_hyss_to_find_the_heavy-atom_substructure_3)
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• dispersive
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• displacement
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm
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  • refinement.htm
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• display_labels
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• free_flags
  • refinement.htm (reflection_output_3)
• free_reflections_per_bin
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• gap_opening_penalty
  • superpose_pdbs.htm (gap_opening_penalty)
• gaussian
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  • autosol.htm (scoring_of_heavy-atom_solutions_12)
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  • phenix-modules.htm
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints)
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  • autobuild.htm (including_ligand_coordinates_in_autobuild_3)
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  • refinement.htm (hydrogens_in_refinement_8)
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  • 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_pdb
  • elbow.htm (additional_programs_2)
• get_smiles
  • elbow.htm (additional_programs_2)
• globulin
  • faqs.htm (what_sample_data_are_available_to_run_automatically__4)
  • examples.htm (what_sample_data_are_available_to_run_automatically__4)
  • tutorial_mr.htm
  • tutorial_mr.htm (introduction_2)
  • tutorial_mr.htm (running_the_demo_a2u-globulin-mr_data_with_automr)
• goto_run
  • running-wizards.htm (keeping_track_of_multiple_runs_of_a_wizard_from_the_gui__6)
  • running-wizards.htm (specific_limitations_and_problems__7)
• gradient
  • phenix-modules.htm (structure_refinement_3)
  • faqs.htm (can_phenix_do_mrsad__4)
  • refinement.htm (refinement_of_coordinates_3)
  • refinement.htm (refinement_of_coordinates_7)
  • refinement.htm (fofc)
• grid_resolution_factor
  • refinement.htm (electron_density_maps_4)
  • refinement.htm (electron_density_maps_5)
  • refinement.htm (grid_resolution_factor)
  • refinement.htm (grid_resolution_factor_1)
  • refinement.htm (grid_resolution_factor_2)
• grid_step
  • refinement.htm (grid_step)
• grid_step_factor
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_5)
  • 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_7)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_12)
  • refinement.htm (refinement_scenarios_3)
  • refinement.htm
  • refinement.htm
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  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_7)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_12)
  • refinement.htm (refinement_scenarios_3)
  • refinement.htm (f_and_f_refinement_4)
  • refinement.htm (f_and_f_refinement_5)
• group_b_iso
  • refinement.htm (min_cross_distance)
• group_ca_length
  • autosol.htm (group_ca_length)
  • autobuild.htm (general_limitations_5)
  • autobuild.htm (group_ca_length)
• group_labels_list
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__3)
  • autosol.htm (group_labels_list)
• group_length
  • autosol.htm (group_length)
  • autobuild.htm (group_length)
• group_occupancy
  • refinement.htm (b_iso_max)
• group_search
  • ligandfit.htm (group_search)
• 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 (sites_file)
  • autosol.htm (ha_sites_file)
• 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_each_possible_space_group__2)
  • autosol.htm (sad_dataset_reading_heavy-atom_sites_from_a_pdb_file_written_by_phenix_hyss_2)
• handedness
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_3)
  • tutorial_mad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_3)
• 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_3)
  • tutorial_mad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_3)
• have_hand
  • autosol.htm (sad_dataset_reading_heavy-atom_sites_from_a_pdb_file_written_by_phenix_hyss_2)
  • autosol.htm (have_hand)
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  • refinement.htm
  • refinement.htm (depositing_refined_structure_with_pdb_3)
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_3)
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_4)
  • phenix_gui.htm (strategies_8)
• headers
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_4)
• height
  • refinement.htm (water_picking_9)
  • xtriage.htm (interpreting_xtriage_output_33)
  • xtriage.htm (interpreting_xtriage_output_52)
  • xtriage.htm (interpreting_xtriage_output_53)
  • xtriage.htm (interpreting_xtriage_output_54)
• helical
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___3)
  • autobuild.htm (input_pdb_file)
  • automr.htm (input_pdb_file)
  • find_helices_strands.htm (how_find_helices_strands_finds_helices_and_strands_in_maps__2)
  • find_helices_strands.htm (how_find_helices_strands_finds_rna_and_dna_helices_in_maps__2)
• helices
  • autobuild.htm (how_the_autobuild_wizard_works_6)
  • autobuild.htm (standard_building_rebuild_in_place_and_multiple-models__3)
  • find_helices_strands.htm
  • find_helices_strands.htm (purpose_2)
  • find_helices_strands.htm (how_find_helices_strands_finds_helices_and_strands_in_maps_)
• helices_only
  • find_helices_strands.htm (helices_only)
• helices_strands_only
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___3)
  • autosol.htm (helices_strands_only)
  • autobuild.htm (helices_strands_only)
  • tutorial_mir.htm (model-building_with_resolve_3)
  • tutorial_mir.htm (how_do_i_know_if_i_have_a_good_solution__3)
• heme
  • autobuild.htm (general_limitations_4)
• 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_3)
  • refinement.htm (relevant_reading_3)
  • autosol.htm (sir__sad_datasets_5)
  • tutorial_mir.htm
  • tutorial_mir.htm (statistical_density_modification_with_resolve_3)
• 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_each_possible_space_group__2)
  • autosol.htm (specific_limitations_and_problems_6)
  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_8)
  • automr.htm (specific_limitations_and_problems_6)
• 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)
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  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__5)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__6)
  • autobuild.htm (and_optional_files_2)
• high_resolution
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_4)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_6)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_7)
  • refinement.htm (refinement_of_coordinates_15)
  • refinement.htm (setting_the_resolution_range_for_the_refinement_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 (edit_pdb)
  • autobuild.htm (highest_resno)
• highest_resolution
  • refinement.htm (grid_step_factor)
  • refinement.htm (grid_step_factor_1)
  • pdbtools.htm (grid_step_factor)
• hires_file
  • autobuild.htm (and_optional_files_2)
  • autobuild.htm (merge_in_hires_data_2)
  • autobuild.htm (hires_file)
• hirshfeld
  • refinement.htm (relevant_reading_3)
  • refinement.htm (rigid_bond_test)
• hklout_denmod
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• hklout_ref
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• hklout_type
  • xtriage.htm (hklout_type)
• hklperfect
  • autosol.htm (hklperfect)
  • autosol.htm (perfect_labels)
  • autosol.htm (use_perfect)
• hl_in_resolve
  • autosol.htm (hl_in_resolve)
• human_readable
  • reflection_file_tools.htm (phenix_mtz_dump_7)
• hydrogen
  • refinement.htm (hydrogens_in_refinement_3)
  • refinement.htm (hydrogens_in_refinement_4)
  • refinement.htm (hydrogens_in_refinement_8)
  • refinement.htm (hydrogens_in_refinement_9)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__3)
• hydrogens
  • refinement.htm
  • refinement.htm
  • refinement.htm
  • refinement.htm (hydrogens_in_refinement)
  • refinement.htm (hydrogens_in_refinement_6)
• 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)
  • autosol.htm
• 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)
• 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 (autobuild_i_ran_seed)
• ias
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
  • 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_17)
  • xtriage.htm (interpreting_xtriage_output_22)
  • xtriage.htm (interpreting_xtriage_output_23)
• id_scale_ref
  • autosol.htm (id_scale_ref)
• ideal
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_12)
  • refinement.htm (xh_bond_distance_deviation_limit)
  • refinement.htm (lattice_symmetry_max_delta_2)
  • xtriage.htm (interpreting_xtriage_output_36)
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_6)
• idealized
  • autosol.htm (hklperfect)
  • tutorial_mir.htm
• ignore_all_zeros
  • refinement.htm (ignore_all_zeros)
  • refinement.htm (ignore_all_zeros_1)
• ignore_blanks
  • autosol.htm (ignore_blanks)
  • autobuild.htm (ignore_blanks)
  • ligandfit.htm (ignore_blanks)
  • automr.htm (ignore_blanks)
• ignore_bulk_solvent_and_scale_failure
  • refinement.htm (ignore_bulk_solvent_and_scale_failure)
• 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)
• ignore_pdb_hexdigest
  • faqs.htm (what_is_an_r-free_flags_mismatch__5)
  • refinement.htm (ignore_pdb_hexdigest)
  • refinement.htm (ignore_pdb_hexdigest_1)
• ignore_r_free_flags
  • refinement.htm (ignoring_test_free_flags_in_refinement_3)
  • 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.h