Author: bugman
Date: Thu Oct 15 12:37:38 2015
New Revision: 28062
URL: http://svn.gna.org/viewcvs/relax?rev=28062&view=rev
Log:
Replicated title fix for the HTML version of the manual.
The replicated titles were causing the sections with the same name to all
point to a single HTML
page with the title name, resulting in a mess in the contents and in the flow
of following the
manual sections sequentially. The relax 4.0.0 documentation has therefore
been especially updated
with these fixes, even though the release does not contain the title name
changes.
Added:
website/manual/Introduction_of_frame_ordering.html
website/manual/Introduction_to_frame_order_data_analysis.html
website/manual/Optimisation_equations_for_the_model_free_analysis.html
website/manual/Optimisation_of_the_frame_order_models.html
website/manual/Simulation_of_the_frame_order_models.html
website/manual/The_current_frame_order_models.html
website/manual/The_frame_order_data_analysis.html
Removed:
website/manual/Data_analysis.html
website/manual/Simulation.html
Modified:
website/manual/A_warning_about_the_formatting.html
website/manual/Abbreviations.html
website/manual/About_this_document.html
website/manual/Access_to_the_internals_of_relax.html
website/manual/Advanced_topics.html
website/manual/All_model_free_models_script_mode_explanation.html
website/manual/All_model_free_models_script_mode_the_sample_script.html
website/manual/Alphabetical_listing_of_user_functions.html
website/manual/Analysing_dispersion_in_the_prompt_script_UI_mode.html
website/manual/Assigning_an_issue_to_yourself.html
website/manual/Becoming_a_committer.html
website/manual/Bibliography.html
website/manual/Branch_creation.html
website/manual/Branches.html
website/manual/Brownian_rotational_diffusion.html
website/manual/C_module_compilation.html
website/manual/Calculating_the_NOE.html
website/manual/Calculation_of_the_NOE_in_the_prompt_script_UI_mode.html
website/manual/Cleaning_up.html
website/manual/Closing_an_issue.html
website/manual/Coding_conventions.html
website/manual/Comments.html
website/manual/Committers.html
website/manual/Comparison_of_dispersion_analysis_software.html
website/manual/Compilation_of_the_API_documentation_HTML_version.html
website/manual/Compilation_of_the_user_manual_HTML_version.html
website/manual/Compilation_of_the_user_manual_PDF_version.html
website/manual/Components_of_the_Ri_theta_equations.html
website/manual/Computation_time_and_the_numerical_integration_of_the_PCS.html
website/manual/Computation_times.html
website/manual/Conjugate_gradient_methods.html
website/manual/Consistency_testing.html
website/manual/Consistency_testing_analysis_references.html
website/manual/Consistency_testing_in_the_prompt_script_UI_mode.html
website/manual/Consistency_testing_script_mode_calculation_and_error_propagation.html
website/manual/Consistency_testing_script_mode_data_pipe_and_spin_system_setup.html
website/manual/Consistency_testing_script_mode_relaxation_data_loading.html
website/manual/Consistency_testing_script_mode_relaxation_interactions.html
website/manual/Consistency_testing_script_mode_the_sample_script.html
website/manual/Consistency_testing_script_mode_visualisation_and_data_output.html
website/manual/Constraint_algorithms.html
website/manual/Construction_of_the_Hessian.html
website/manual/Construction_of_the_gradient.html
website/manual/Construction_of_the_values_gradients_and_Hessians.html
website/manual/Contents.html
website/manual/Copying_modification_sublicencing_and_distribution_of_relax.html
website/manual/Dasha.html
website/manual/Data_analysis_tools.html
website/manual/Data_visualisation.html
website/manual/Defaults.html
website/manual/Dependencies.html
website/manual/Derivation_of_a_2D_trigonometric_function_the_pseudo_elliptic_cosine.html
website/manual/Determining_stereochemistry_in_dynamic_molecules.html
website/manual/Diagonal_scaling.html
website/manual/Discussing_major_changes.html
website/manual/Dispersion_GUI_mode_choosing_the_models_to_optimise.html
website/manual/Dispersion_GUI_mode_comparing_models.html
website/manual/Dispersion_GUI_mode_comparison_of_the_analyses.html
website/manual/Dispersion_GUI_mode_computation_time.html
website/manual/Dispersion_GUI_mode_dispersion_setup.html
website/manual/Dispersion_GUI_mode_execution_of_the_non_clustered_analysis.html
website/manual/Dispersion_GUI_mode_general_setup.html
website/manual/Dispersion_GUI_mode_initialisation_of_the_data_pipe.html
website/manual/Dispersion_GUI_mode_inspection_of_the_results.html
website/manual/Dispersion_GUI_mode_loading_the_data.html
website/manual/Dispersion_GUI_mode_optimisation_settings.html
website/manual/Dispersion_GUI_mode_setting_up_the_spin_systems.html
website/manual/Dispersion_GUI_mode_the_clustered_analysis.html
website/manual/Dispersion_GUI_mode_two_analyses.html
website/manual/Dispersion_GUI_mode_unresolved_spins.html
website/manual/Dispersion_curve_insignificance.html
website/manual/Dispersion_model_summary.html
website/manual/Dispersion_parameter_grid_search.html
website/manual/Dispersion_parameter_optimisation.html
website/manual/Dispersion_script_mode_analysis_variables.html
website/manual/Dispersion_script_mode_execution.html
website/manual/Dispersion_script_mode_imports.html
website/manual/Dispersion_script_mode_initialisation_of_the_data_pipe.html
website/manual/Dispersion_script_mode_loading_the_data.html
website/manual/Dispersion_script_mode_setting_up_the_spin_systems.html
website/manual/Dispersion_script_mode_the_rest_of_the_setup.html
website/manual/Dispersion_script_mode_the_sample_script.html
website/manual/Doc_strings.html
website/manual/Docstring_sectioning.html
website/manual/Double_pivoted_motions.html
website/manual/Double_rotor_equations.html
website/manual/Double_rotor_frame_order_model.html
website/manual/Double_rotor_parameterisation.html
website/manual/Ellipsoidal_diffusion_tensor.html
website/manual/Ellipsoidal_dot_product_derivatives.html
website/manual/Error_analysis.html
website/manual/Experimental_data_support_for_the_N_state_model.html
website/manual/Final_checks_of_the_curve_fitting.html
website/manual/Format_of_the_commit_logs.html
website/manual/Frame_order.html
website/manual/Frame_order_and_the_alignment_tensor.html
website/manual/Frame_order_axis_permutations.html
website/manual/Frame_order_in_rotational_Brownian_diffusion_and_NMR_relaxation.html
website/manual/Frame_order_model_nesting.html
website/manual/Frame_order_modelling.html
website/manual/Frame_order_theory.html
website/manual/Free_rotor_equations.html
website/manual/Free_rotor_frame_order_model.html
website/manual/Free_rotor_isotropic_cone_equations.html
website/manual/Free_rotor_isotropic_cone_frame_order_model.html
website/manual/Free_rotor_isotropic_cone_parameterisation.html
website/manual/Free_rotor_parameterisation.html
website/manual/Free_rotor_pseudo_ellipse_equations.html
website/manual/Free_rotor_pseudo_ellipse_frame_order_model.html
website/manual/Free_rotor_pseudo_ellipse_parameterisation.html
website/manual/From_spectra_to_peak_intensities_for_the_NOE.html
website/manual/From_spectra_to_peak_intensities_for_the_relaxation_rates.html
website/manual/Further_details.html
website/manual/GUI_mode_deselect_spins.html
website/manual/GUI_mode_manual_construction.html
website/manual/GUI_mode_setting_up_the_data_pipe.html
website/manual/GUI_mode_spins_from_a_sequence_file.html
website/manual/GUI_mode_spins_from_structural_data.html
website/manual/Generic_parts_of_relax.html
website/manual/Grace.html
website/manual/Graphical_user_interface_reference.html
website/manual/Hessian_modifications.html
website/manual/How_to_use_relax.html
website/manual/Implementation.html
website/manual/Implemented_models.html
website/manual/Indentation.html
website/manual/Index.html
website/manual/Installation.html
website/manual/Installation_instructions.html
website/manual/Installation_on_GNU_Linux.html
website/manual/Installation_on_MS_Windows.html
website/manual/Installation_on_Mac_OS_X.html
website/manual/Installation_on_your_OS.html
website/manual/Interatomic_data_containers.html
website/manual/Interfacing_with_other_programs.html
website/manual/Introduction.html
website/manual/Introduction_to_reduced_spectral_density_mapping.html
website/manual/Introduction_to_relaxation_curve_fitting.html
website/manual/Introduction_to_relaxation_dispersion.html
website/manual/Introduction_to_the_N_state_model.html
website/manual/Introduction_to_the_consistency_testing_of_relaxation_data.html
website/manual/Introduction_to_the_mathematics_behind_the_optimisation_of_relaxation_data.html
website/manual/Introduction_to_the_multi_processor.html
website/manual/Introduction_to_the_steady_state_NOE.html
website/manual/Isotropic_cone_equations.html
website/manual/Isotropic_cone_frame_order_model.html
website/manual/Isotropic_cone_parameterisation.html
website/manual/J_w_mapping_script_mode_calculation_and_error_propagation.html
website/manual/J_w_mapping_script_mode_data_pipe_and_spin_system_setup.html
website/manual/J_w_mapping_script_mode_relaxation_data_loading.html
website/manual/J_w_mapping_script_mode_relaxation_interactions.html
website/manual/J_w_mapping_script_mode_the_sample_script.html
website/manual/J_w_mapping_script_mode_visualisation_and_data_output.html
website/manual/Joining_Gna.html
website/manual/Joining_the_relax_project.html
website/manual/Keeping_the_branch_up_to_date_using_svnmerge_py.html
website/manual/Latest_sources_the_relax_repositories.html
website/manual/Licence.html
website/manual/Line_search_methods.html
website/manual/Linear_constraints_for_the_frame_order_models.html
website/manual/Links_links_and_more_links.html
website/manual/List_of_Figures.html
website/manual/List_of_Tables.html
website/manual/Literature.html
website/manual/Ln3_aligned_RDC_and_PCS_data.html
website/manual/Logarithmic_barrier_constraint_algorithm.html
website/manual/Making_distribution_archives.html
website/manual/Measuring_peak_intensities.html
website/manual/Merging_the_branch_back_into_the_main_line.html
website/manual/Method_of_Multipliers_algorithm.html
website/manual/Model_free_analysis.html
website/manual/Model_free_analysis_in_reverse.html
website/manual/Model_free_analysis_references.html
website/manual/Model_free_model_selection.html
website/manual/Model_free_model_selection_script_mode_explanation.html
website/manual/Model_free_model_selection_script_mode_the_sample_script.html
website/manual/Model_free_optimisation_theory.html
website/manual/Model_free_theory.html
website/manual/Model_selection_references.html
website/manual/Modelfree4.html
website/manual/Modification_of_official_releases_creating_patches_with_diff.html
website/manual/Modification_of_the_latest_sources_creating_patches_with_Subversion.html
website/manual/Molecule_residue_and_spin_containers.html
website/manual/Molmol.html
website/manual/Monte_Carlo_simulation_elimination.html
website/manual/NOE_GUI_mode_general_setup.html
website/manual/NOE_GUI_mode_initialisation_of_the_data_pipe.html
website/manual/NOE_GUI_mode_loading_the_data.html
website/manual/NOE_GUI_mode_setting_up_the_spin_systems.html
website/manual/NOE_GUI_mode_the_NOE_calculation.html
website/manual/NOE_GUI_mode_unresolved_spins.html
website/manual/NOE_script_mode_initialisation_of_the_data_pipe.html
website/manual/NOE_script_mode_loading_the_data.html
website/manual/NOE_script_mode_setting_the_errors.html
website/manual/NOE_script_mode_setting_up_the_spin_systems.html
website/manual/NOE_script_mode_the_NOE_calculation.html
website/manual/NOE_script_mode_the_sample_script.html
website/manual/NOE_script_mode_unresolved_spins.html
website/manual/NOE_script_mode_viewing_the_results.html
website/manual/NOEs_in_the_N_state_model.html
website/manual/N_state_model_analysis_references.html
website/manual/Navigation.html
website/manual/News.html
website/manual/Numerical_integration_techniques.html
website/manual/OpenDX.html
website/manual/Open_source_infrastructure.html
website/manual/Optimisation.html
website/manual/Optimisation_algorithms.html
website/manual/Optimisation_of_a_single_model_free_model.html
website/manual/Optimisation_of_all_model_free_models.html
website/manual/Optimisation_of_relaxation_data_values_gradients_and_Hessians.html
website/manual/Optimisation_of_the_diffusion_tensor_parameters.html
website/manual/Optimisation_of_the_global_model.html
website/manual/Optimisation_of_the_local_tau_m_models.html
website/manual/Optimisation_of_the_model_free_models.html
website/manual/Optional_programs.html
website/manual/Other_citations.html
website/manual/Other_methods.html
website/manual/PCS_subset.html
website/manual/PCSs_in_the_N_state_model.html
website/manual/Parallelization_and_running_on_a_cluster.html
website/manual/Power_users.html
website/manual/Preface_citing_relax.html
website/manual/Private_vs_public_messages.html
website/manual/Program_features.html
website/manual/Pseudo_ellipse_equations.html
website/manual/Pseudo_ellipse_frame_order_model.html
website/manual/Pseudo_ellipse_parameterisation.html
website/manual/PyMOL.html
website/manual/Python.html
website/manual/RDCs_in_the_N_state_model.html
website/manual/Reduced_spectral_density_mapping.html
website/manual/Reduced_spectral_density_mapping_references.html
website/manual/Reference.html
website/manual/Relax_fit_GUI_mode_general_setup.html
website/manual/Relax_fit_GUI_mode_initialisation_of_the_data_pipe.html
website/manual/Relax_fit_GUI_mode_loading_the_data.html
website/manual/Relax_fit_GUI_mode_optimisation_and_error_analysis.html
website/manual/Relax_fit_GUI_mode_setting_up_the_spin_systems.html
website/manual/Relax_fit_GUI_mode_unresolved_spins.html
website/manual/Relax_fit_script_mode_error_analysis.html
website/manual/Relax_fit_script_mode_finishing_off.html
website/manual/Relax_fit_script_mode_initialisation_of_the_data_pipe.html
website/manual/Relax_fit_script_mode_loading_the_data.html
website/manual/Relax_fit_script_mode_optimisation_of_exponential_curves.html
website/manual/Relax_fit_script_mode_setting_up_the_spin_systems.html
website/manual/Relax_fit_script_mode_the_rest_of_the_setup.html
website/manual/Relax_fit_script_mode_the_sample_script.html
website/manual/Relaxation_curve_fitting.html
website/manual/Relaxation_curve_fitting_in_the_prompt_script_UI_mode.html
website/manual/Relaxation_dispersion.html
website/manual/Relaxation_dispersion_diagonal_scaling.html
website/manual/Relaxation_dispersion_model_elimination.html
website/manual/Relaxation_dispersion_on_a_computer_cluster_using_OpenMPI.html
website/manual/Relaxation_dispersion_optimisation_theory.html
website/manual/Relaxation_dispersion_parameter_constraints.html
website/manual/Relaxation_dispersion_references.html
website/manual/Replying_to_a_message.html
website/manual/Reporting_bugs.html
website/manual/Ri_theta_Hessians.html
website/manual/Ri_theta_gradients.html
website/manual/Ri_theta_values.html
website/manual/Ri_theta_values_gradients_and_Hessians.html
website/manual/Rigid_body_motions_for_a_two_domain_system.html
website/manual/Rigid_frame_order_model.html
website/manual/Rigid_model_equations.html
website/manual/Rigid_model_parameterisation.html
website/manual/Rotor_equations.html
website/manual/Rotor_frame_order_model.html
website/manual/Rotor_parameterisation.html
website/manual/Running_a_non_compiled_version.html
website/manual/SCons_help.html
website/manual/Script_mode_manual_construction.html
website/manual/Script_mode_spins_from_a_sequence_file.html
website/manual/Script_mode_spins_from_structural_data.html
website/manual/Scripting.html
website/manual/Search_engine_indexing.html
website/manual/Setup_in_the_GUI.html
website/manual/Setup_in_the_prompt_script_UI.html
website/manual/Single_model_free_model_script_mode_explanation.html
website/manual/Single_model_free_model_script_mode_the_sample_script.html
website/manual/Single_pivoted_motions.html
website/manual/Specific_analyses.html
website/manual/Spectral_processing.html
website/manual/Spherical_diffusion_tensor.html
website/manual/Spheroidal_diffusion_tensor.html
website/manual/Spheroidal_dot_product_derivatives.html
website/manual/Stereochemistry_the_auto_analysis.html
website/manual/Stereochemistry_the_sample_script.html
website/manual/Submitting_a_bug_report.html
website/manual/Submitting_changes_as_a_patch.html
website/manual/Submitting_changes_to_the_relax_project.html
website/manual/Supported_NMR_theories.html
website/manual/Tab_completion.html
website/manual/Temperature_control_and_calibration.html
website/manual/Tensors_of_frame_ordering.html
website/manual/The_DPL94_2_site_fast_exchange_R1_rho_model.html
website/manual/The_GPL.html
website/manual/The_GUI.html
website/manual/The_Hessian.html
website/manual/The_IT99_2_site_CPMG_model.html
website/manual/The_LM63_2_site_fast_exchange_CPMG_model.html
website/manual/The_LM63_3_site_fast_exchange_CPMG_model.html
website/manual/The_M61_2_site_fast_exchange_R1_rho_model.html
website/manual/The_M61_skew_2_site_fast_exchange_R1_rho_model.html
website/manual/The_MMQ_CR72_model.html
website/manual/The_MP05_2_site_exchange_R1_rho_model.html
website/manual/The_NOE_auto_analysis_in_the_GUI.html
website/manual/The_NS_2_site_R1_rho_model.html
website/manual/The_NS_2_site_expanded_CPMG_model.html
website/manual/The_NS_3_site_R1_rho_model.html
website/manual/The_NS_3_site_linear_R1_rho_model.html
website/manual/The_NS_MMQ_2_site_model.html
website/manual/The_NS_MMQ_3_site_linear_model.html
website/manual/The_NS_MMQ_3_site_model.html
website/manual/The_N_state_model_analysis_scripts.html
website/manual/The_N_state_model_or_ensemble_analysis.html
website/manual/The_R2eff_model.html
website/manual/The_Ri_theta_Hessians.html
website/manual/The_Ri_theta_gradients.html
website/manual/The_Ri_theta_values.html
website/manual/The_Ri_theta_values_gradients_and_Hessians.html
website/manual/The_SCons_build_system.html
website/manual/The_TAP03_2_site_exchange_R1_rho_model.html
website/manual/The_TP02_2_site_exchange_R1_rho_model.html
website/manual/The_TSMFK01_2_site_CPMG_model.html
website/manual/The_alternative_extended_model_free_Hessian.html
website/manual/The_alternative_extended_model_free_gradient.html
website/manual/The_analytic_CPMG_models.html
website/manual/The_analytic_MMQ_CPMG_models.html
website/manual/The_analytic_R1_rho_models.html
website/manual/The_base_dispersion_models.html
website/manual/The_basics.html
website/manual/The_bug_task_and_support_request_trackers.html
website/manual/The_chi_2_Hessian.html
website/manual/The_chi_2_gradient.html
website/manual/The_chi_2_value.html
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