Contents

• List of Figures
• List of Tables
  • Preface - citing relax
  
  
• The basics
  • Introduction
    • Program features
      • Literature
      • Supported NMR theories
      • Data analysis tools
      • Data visualisation
      • Interfacing with other programs
      • The user interfaces (UI)
    • How to use relax
      • The prompt
      • Python
      • User functions
      • The help system
      • Tab completion
      • The data pipe
      • The spin and interatomic data containers
      • Scripting
      • The test suite
      • The GUI
      • Access to the internals of relax
    • The multi-processor framework
      • Introduction to the multi-processor
      • Usage of the multi-processor
      • Further details
    • Usage of the name relax
  • Installation instructions
    • Dependencies
    • Installation
      • The source releases
      • Installation on GNU/Linux
      • Installation on MS Windows
      • Installation on Mac OS X
      • Installation on your OS
      • Running a non-compiled version
    • Optional programs
      • Grace
      • OpenDX
      • Molmol
      • PyMOL
      • Dasha
      • Modelfree4
  • Free software infrastructure
    • History
    • The relax web sites
    • The mailing lists
      • relax-announce
      • relax-users
      • relax-devel
      • relax-commits
      • Replying to a message
    • Reporting bugs
    • Latest sources - the relax repositories
    • The relax distribution archives
  • The relax data model
    • The concept of the relax data model
    • The data model
      • The relax data store
      • Molecule, residue, and spin containers
    • Interatomic data containers
    • Setup in the prompt/script UI
      • Script mode - spins from structural data
      • Script mode - spins from a sequence file
      • Script mode - manual construction
    • Setup in the GUI
      • GUI mode - setting up the data pipe
      • GUI mode - spins from structural data
      • GUI mode - spins from a sequence file
      • GUI mode - manual construction
      • GUI mode - deselect spins
    • The next steps
  
  
• The specific analyses
  • The R₁ and R₂ relaxation rates - relaxation curve-fitting
    • Introduction to relaxation curve-fitting
    • The exponential curve models
    • From spectra to peak intensities for the relaxation rates
      • Temperature control and calibration
      • Spectral processing
      • Measuring peak intensities
    • Relaxation curve-fitting in the prompt/script UI mode
      • Relax-fit script mode - the sample script
      • Relax-fit script mode - initialisation of the data pipe
      • Relax-fit script mode - setting up the spin systems
      • Relax-fit script mode - loading the data
      • Relax-fit script mode - the rest of the setup
      • Relax-fit script mode - optimisation of exponential curves
      • Relax-fit script mode - error analysis
      • Relax-fit script mode - finishing off
    • The relaxation curve-fitting auto-analysis in the GUI
      • Relax-fit GUI mode - initialisation of the data pipe
      • Relax-fit GUI mode - general setup
      • Relax-fit GUI mode - setting up the spin systems
      • Relax-fit GUI mode - unresolved spins
      • Relax-fit GUI mode - loading the data
      • Relax-fit GUI mode - optimisation and error analysis
    • Final checks of the curve-fitting
  • Calculating the NOE
    • Introduction to the steady-state NOE
    • From spectra to peak intensities for the NOE
    • Calculation of the NOE in the prompt/script UI mode
      • NOE script mode - the sample script
      • NOE script mode - initialisation of the data pipe
      • NOE script mode - setting up the spin systems
      • NOE script mode - loading the data
      • NOE script mode - setting the errors
      • NOE script mode - unresolved spins
      • NOE script mode - the NOE calculation
      • NOE script mode - viewing the results
    • The NOE auto-analysis in the GUI
      • NOE GUI mode - initialisation of the data pipe
      • NOE GUI mode - general setup
      • NOE GUI mode - setting up the spin systems
      • NOE GUI mode - unresolved spins
      • NOE GUI mode - loading the data
      • NOE GUI mode - the NOE calculation
  • Model-free analysis
    • Model-free theory
      • The chi-squared function - χ²(θ)
      • The transformed relaxation equations - R_i(θ)
      • The relaxation equations - R_i'(θ)
      • The spectral density functions - J(ω)
      • Brownian rotational diffusion
      • The model-free models
      • Model-free optimisation theory
    • Optimisation of a single model-free model
      • Single model-free model script mode - the sample script
      • Single model-free model script mode - explanation
    • Optimisation of all model-free models
      • All model-free models script mode - the sample script
      • All model-free models script mode - explanation
    • Model-free model selection
      • Model-free model selection script mode - the sample script
      • Model-free model selection script mode - explanation
    • The methodology of Mandel et al., 1995
    • The diffusion seeded paradigm
    • The new model-free optimisation protocol
      • The new protocol - model-free models
      • The new protocol - the diffusion tensor
      • The universal solution U
      • Model-free analysis in reverse
    • The new protocol in the prompt/script UI mode
      • d'Auvergne protocol script mode - the sample script
      • d'Auvergne protocol script mode - analysis variables
      • d'Auvergne protocol script mode - data pipe initialisation
      • d'Auvergne protocol script mode - setting up the spin systems
      • d'Auvergne protocol script mode - loading the data
      • d'Auvergne protocol script mode - deselection
      • d'Auvergne protocol script mode - relaxation interactions
      • d'Auvergne protocol script mode - execution
    • The new protocol in the GUI
      • d'Auvergne protocol GUI mode - data pipe initialisation
      • d'Auvergne protocol GUI mode - general setup
      • d'Auvergne protocol GUI mode - setting up the spin systems
      • d'Auvergne protocol GUI mode - unresolved spins
      • d'Auvergne protocol GUI mode - loading the data
      • d'Auvergne protocol GUI mode - relaxation interactions
      • d'Auvergne protocol GUI mode - spin isotopes
      • d'Auvergne protocol GUI mode - the rest of the setup
      • d'Auvergne protocol GUI mode - execution
      • d'Auvergne protocol GUI mode - completion
      • d'Auvergne protocol GUI mode - BMRB deposition
  • Reduced spectral density mapping
    • Introduction to reduced spectral density mapping
    • J(w) mapping script mode - the sample script
    • J(w) mapping script mode - data pipe and spin system setup
    • J(w) mapping script mode - relaxation data loading
    • J(w) mapping script mode - relaxation interactions
    • J(w) mapping script mode - calculation and error propagation
    • J(w) mapping script mode - visualisation and data output
  • Consistency testing
    • Introduction to the consistency testing of relaxation data
    • Consistency testing in the prompt/script UI mode
      • Consistency testing script mode - the sample script
    • Consistency testing script mode - data pipe and spin system setup
    • Consistency testing script mode - relaxation data loading
    • Consistency testing script mode - relaxation interactions
    • Consistency testing script mode - calculation and error propagation
    • Consistency testing script mode - visualisation and data output
  • The N-state model or ensemble analysis
    • Introduction to the N-state model
    • Experimental data support for the N-state model
      • RDCs in the N-state model
      • PCSs in the N-state model
      • NOEs in the N-state model
    • Determining stereochemistry in dynamic molecules
      • Stereochemistry - the auto-analysis
      • Stereochemistry - the sample script
  • The analysis of relaxation dispersion
    • Introduction to relaxation dispersion
      • The modelling of dispersion data
      • Implemented models
      • Dispersion model summary
    • The base dispersion models
      • The R2eff model
      • The model for no chemical exchange relaxation
    • The analytic CPMG models
      • The LM63 2-site fast exchange CPMG model
      • The LM63 3-site fast exchange CPMG model
      • The full CR72 2-site CPMG model
      • The reduced CR72 2-site CPMG model
      • The IT99 2-site CPMG model
      • The TSMFK01 2-site CPMG model
      • The full B14 2-site CPMG model
      • The reduced B14 2-site CPMG model
    • The numeric CPMG models
      • The NS 2-site expanded CPMG model
      • The full NS 2-site 3D CPMG model
      • The reduced NS 2-site 3D CPMG model
      • The full NS 2-site star CPMG model
      • The reduced NS 2-site star CPMG model
    • The analytic MMQ CPMG models
      • The MMQ CR72 model
    • The numeric MMQ CPMG models
      • The NS MMQ 2-site model
      • The NS MMQ 3-site linear model
      • The NS MMQ 3-site model
    • The analytic R_1ρ models
      • The M61 2-site fast exchange R_1ρ model
      • The M61 skew 2-site fast exchange R_1ρ model
      • The DPL94 2-site fast exchange R_1ρ model
      • The TP02 2-site exchange R_1ρ model
      • The TAP03 2-site exchange R_1ρ model
      • The MP05 2-site exchange R_1ρ model
    • The numeric R_1ρ models
      • The NS 2-site R_1ρ model
      • The NS 3-site R_1ρ model
      • The NS 3-site linear R_1ρ model
    • Relaxation dispersion optimisation theory
      • The relaxation dispersion auto-analysis
      • Dispersion curve insignificance
      • The relaxation dispersion space
      • The clustered relaxation dispersion analysis
      • Dispersion parameter grid search
      • Dispersion parameter optimisation
      • Relaxation dispersion parameter constraints
      • Relaxation dispersion diagonal scaling
      • Relaxation dispersion model elimination
      • Monte Carlo simulation elimination
      • Relaxation dispersion on a computer cluster using OpenMPI
    • To do - dispersion features yet to be implemented
    • Tutorial for adding relaxation dispersion models
    • Comparison of dispersion analysis software
    • Analysing dispersion in the prompt/script UI mode
      • Dispersion script mode - the sample script
      • Dispersion script mode - imports
      • Dispersion script mode - analysis variables
      • Dispersion script mode - initialisation of the data pipe
      • Dispersion script mode - setting up the spin systems
      • Dispersion script mode - loading the data
      • Dispersion script mode - the rest of the setup
      • Dispersion script mode - execution
    • The relaxation dispersion auto-analysis in the GUI
      • Dispersion GUI mode - two analyses
      • Dispersion GUI mode - computation time
      • Dispersion GUI mode - initialisation of the data pipe
      • Dispersion GUI mode - general setup
      • Dispersion GUI mode - setting up the spin systems
      • Dispersion GUI mode - unresolved spins
      • Dispersion GUI mode - dispersion setup
      • Dispersion GUI mode - loading the data
      • Dispersion GUI mode - choosing the models to optimise
      • Dispersion GUI mode - optimisation settings
      • Dispersion GUI mode - execution of the non-clustered analysis
      • Dispersion GUI mode - inspection of the results
      • Dispersion GUI mode - comparing models
      • Dispersion GUI mode - the clustered analysis
      • Dispersion GUI mode - comparison of the analyses
  • The ordering of frames
    • Introduction of frame ordering
      • Tensors of frame ordering
      • Ln³⁺ aligned RDC and PCS data
    • Frame order theory
      • Frame order introduction
      • Frame order and the alignment tensor
      • Single pivoted motions
      • Double pivoted motions
      • Frame order in rotational Brownian diffusion and NMR relaxation
    • Frame order modelling
      • Rigid body motions for a two domain system
      • Frame order axis permutations
      • Linear constraints for the frame order models
    • Computation time and the numerical integration of the PCS
      • Numerical integration techniques
      • Parallelization and running on a cluster
      • Frame order model nesting
      • PCS subset
      • Optimisation of the frame order models
      • Error analysis
    • The frame order data analysis
      • Introduction to frame order data analysis
      • The N-state model analysis scripts
      • The frame order analysis scripts
      • Computation times
  
  
• Power users
  • relax development
    • The relax source code repositories
      • relax repositories
      • Primary relax repository
      • Mirrors of the relax repository
    • Coding conventions
      • Indentation
      • Doc strings
      • Variable, function, and class names
      • Whitespace
      • Comments
    • Committers
      • Becoming a committer
      • Register for a relax infrastructure account
      • Joining the relax project
      • Format of the commit logs
      • Discussing major changes
    • Submitting changes to the relax project
      • Development branches
      • Keeping the branch up to date
      • Submitting patches
      • Repository forks
      • Merging the branch back into the main line
    • The SCons build system
      • SCons help
      • C module compilation
      • Compilation of the user manual (PDF version)
      • Compilation of the user manual (HTML version)
      • Compilation of the API documentation (HTML version)
      • Making distribution archives
      • Cleaning up
    • The core design of relax
      • The divisions of relax's source code
      • The major components of relax
    • The mailing lists for development
      • Private vs. public messages
    • The bug, task, and support request trackers
      • Submitting a bug report
      • Assigning an issue to yourself
      • Closing an issue
    • Links, links, and more links
      • Navigation
      • Search engine indexing
  
  
• Advanced topics
  • Optimisation
    • Implementation
      • The interface
      • The minfx package
    • The optimisation space
    • Topology of the space
      • The function value
      • The gradient
      • The Hessian
    • Optimisation algorithms
      • Line search methods
      • Trust region methods
      • Conjugate gradient methods
      • Hessian modifications
      • Other methods
    • Constraint algorithms
      • Method of Multipliers algorithm
      • Logarithmic barrier constraint algorithm
    • Diagonal scaling
  • Optimisation of relaxation data - values, gradients, and Hessians
    • Introduction to the mathematics behind the optimisation of relaxation data
    • The four parameter combinations
      • Optimisation of the model-free models
      • Optimisation of the local τ_m models
      • Optimisation of the diffusion tensor parameters
      • Optimisation of the global model
    • Construction of the values, gradients, and Hessians
      • The sum of chi-squared values
      • Construction of the gradient
      • Construction of the Hessian
    • The value, gradient, and Hessian dependency chain
    • The χ² value, gradient, and Hessian
      • The χ² value
      • The χ² gradient
      • The χ² Hessian
    • The R_i(θ) values, gradients, and Hessians
      • The R_i(θ) values
      • The R_i(θ) gradients
      • The R_i(θ) Hessians
    • R_i'(θ) values, gradients, and Hessians
      • Components of the R_i'(θ) equations
      • R_i'(θ) values
      • R_i'(θ) gradients
      • R_i'(θ) Hessians
    • Optimisation equations for the model-free analysis
      • The model-free equations
      • The original model-free gradient
      • The original model-free Hessian
      • The extended model-free gradient
      • The extended model-free Hessian
      • The alternative extended model-free gradient
      • The alternative extended model-free Hessian
    • Ellipsoidal diffusion tensor
      • The diffusion equation of the ellipsoid
      • The weights of the ellipsoid
      • The weight gradients of the ellipsoid
      • The weight Hessians of the ellipsoid
      • The correlation times of the ellipsoid
      • The correlation time gradients of the ellipsoid
      • The correlation time Hessians of the ellipsoid
    • Spheroidal diffusion tensor
      • The diffusion equation of the spheroid
      • The weights of the spheroid
      • The weight gradients of the spheroid
      • The weight Hessians of the spheroid
      • The correlation times of the spheroid
      • The correlation time gradients of the spheroid
      • The correlation time Hessians of the spheroid
    • Spherical diffusion tensor
      • The diffusion equation of the sphere
      • The weight of the sphere
      • The weight gradient of the sphere
      • The weight Hessian of the sphere
      • The correlation time of the sphere
      • The correlation time gradient of the sphere
      • The correlation time Hessian of the sphere
    • Ellipsoidal dot product derivatives
      • The dot product of the ellipsoid
      • The dot product gradient of the ellipsoid
      • The dot product Hessian of the ellipsoid
    • Spheroidal dot product derivatives
      • The dot product of the spheroid
      • The dot product gradient of the spheroid
      • The dot product Hessian of the spheroid
  • The frame order models
    • The current frame order models
    • Simulation of the frame order models
    • Rigid frame order model
      • Rigid model parameterisation
      • Rigid model equations
    • Rotor frame order model
      • Rotor parameterisation
      • Rotor equations
    • Free rotor frame order model
      • Free rotor parameterisation
      • Free rotor equations
    • Isotropic cone frame order model
      • Isotropic cone parameterisation
      • Isotropic cone equations
    • Torsionless isotropic cone frame order model
      • Torsionless isotropic cone parameterisation
      • Torsionless isotropic cone equations
    • Free rotor isotropic cone frame order model
      • Free rotor isotropic cone parameterisation
      • Free rotor isotropic cone equations
    • Pseudo-ellipse frame order model
      • Pseudo-ellipse parameterisation
      • Derivation of a 2D trigonometric function - the pseudo-elliptic cosine
      • Pseudo-ellipse equations
    • Torsionless pseudo-ellipse frame order model
      • Torsionless pseudo-ellipse parameterisation
      • Torsionless pseudo-ellipse equations
    • Free rotor pseudo-ellipse frame order model
      • Free rotor pseudo-ellipse parameterisation
      • Free rotor pseudo-ellipse equations
    • Double rotor frame order model
      • Double rotor parameterisation
      • Double rotor equations
  
  
• Reference
  • Alphabetical listing of user functions
    • A warning about the formatting
    • The list of functions
      • The synopsis
      • Defaults
      • Docstring sectioning
      • align_tensor.copy
      • align_tensor.delete
      • align_tensor.display
      • align_tensor.fix
      • align_tensor.init
      • align_tensor.matrix_angles
      • align_tensor.reduction
      • align_tensor.set_domain
      • align_tensor.svd
      • angles.diff_frame
      • bmrb.citation
      • bmrb.display
      • bmrb.read
      • bmrb.script
      • bmrb.software
      • bmrb.software_select
      • bmrb.thiol_state
      • bmrb.write
      • bruker.read
      • chemical_shift.read
      • consistency_tests.set_frq
      • dasha.create
      • dasha.execute
      • dasha.extract
      • deselect.all
      • deselect.interatom
      • deselect.read
      • deselect.reverse
      • deselect.sn_ratio
      • deselect.spin
      • diffusion_tensor.copy
      • diffusion_tensor.delete
      • diffusion_tensor.display
      • diffusion_tensor.init
      • domain
      • dx.execute
      • dx.map
      • eliminate
      • error_analysis.covariance_matrix
      • fix
      • frame_order.count_sobol_points
      • frame_order.decompose
      • frame_order.distribute
      • frame_order.pdb_model
      • frame_order.permute_axes
      • frame_order.pivot
      • frame_order.quad_int
      • frame_order.ref_domain
      • frame_order.select_model
      • frame_order.simulate
      • frame_order.sobol_setup
      • grace.view
      • grace.write
      • interatom.copy
      • interatom.define
      • interatom.read_dist
      • interatom.set_dist
      • interatom.unit_vectors
      • j_coupling.copy
      • j_coupling.delete
      • j_coupling.display
      • j_coupling.read
      • j_coupling.write
      • jw_mapping.set_frq
      • minimise.calculate
      • minimise.execute
      • minimise.grid_search
      • minimise.grid_zoom
      • model_free.create_model
      • model_free.delete
      • model_free.remove_tm
      • model_free.select_model
      • model_selection
      • molecule.copy
      • molecule.create
      • molecule.delete
      • molecule.display
      • molecule.name
      • molecule.type
      • molmol.clear_history
      • molmol.command
      • molmol.macro_apply
      • molmol.macro_run
      • molmol.macro_write
      • molmol.ribbon
      • molmol.tensor_pdb
      • molmol.view
      • monte_carlo.create_data
      • monte_carlo.error_analysis
      • monte_carlo.initial_values
      • monte_carlo.off
      • monte_carlo.on
      • monte_carlo.setup
      • n_state_model.CoM
      • n_state_model.cone_pdb
      • n_state_model.elim_no_prob
      • n_state_model.number_of_states
      • n_state_model.ref_domain
      • n_state_model.select_model
      • noe.read_restraints
      • noe.spectrum_type
      • palmer.create
      • palmer.execute
      • palmer.extract
      • paramag.centre
      • pcs.back_calc
      • pcs.calc_q_factors
      • pcs.copy
      • pcs.corr_plot
      • pcs.delete
      • pcs.display
      • pcs.read
      • pcs.set_errors
      • pcs.structural_noise
      • pcs.weight
      • pcs.write
      • pipe.bundle
      • pipe.change_type
      • pipe.copy
      • pipe.create
      • pipe.current
      • pipe.delete
      • pipe.display
      • pipe.hybridise
      • pipe.switch
      • pymol.cartoon
      • pymol.clear_history
      • pymol.command
      • pymol.cone_pdb
      • pymol.frame_order
      • pymol.macro_apply
      • pymol.macro_run
      • pymol.macro_write
      • pymol.tensor_pdb
      • pymol.vector_dist
      • pymol.view
      • rdc.back_calc
      • rdc.calc_q_factors
      • rdc.copy
      • rdc.corr_plot
      • rdc.delete
      • rdc.display
      • rdc.read
      • rdc.set_errors
      • rdc.weight
      • rdc.write
      • relax_data.back_calc
      • relax_data.copy
      • relax_data.delete
      • relax_data.display
      • relax_data.peak_intensity_type
      • relax_data.read
      • relax_data.temp_calibration
      • relax_data.temp_control
      • relax_data.type
      • relax_data.write
      • relax_disp.catia_execute
      • relax_disp.catia_input
      • relax_disp.cluster
      • relax_disp.cpmg_setup
      • relax_disp.cpmgfit_execute
      • relax_disp.cpmgfit_input
      • relax_disp.exp_type
      • relax_disp.insignificance
      • relax_disp.nessy_input
      • relax_disp.parameter_copy
      • relax_disp.plot_disp_curves
      • relax_disp.plot_exp_curves
      • relax_disp.r1_fit
      • relax_disp.r20_from_min_r2eff
      • relax_disp.r2eff_err_estimate
      • relax_disp.r2eff_read
      • relax_disp.r2eff_read_spin
      • relax_disp.relax_time
      • relax_disp.select_model
      • relax_disp.sherekhan_input
      • relax_disp.spin_lock_field
      • relax_disp.spin_lock_offset
      • relax_disp.write_disp_curves
      • relax_fit.relax_time
      • relax_fit.select_model
      • reset
      • residue.copy
      • residue.create
      • residue.delete
      • residue.display
      • residue.name
      • residue.number
      • results.display
      • results.read
      • results.write
      • script
      • select.all
      • select.display
      • select.domain
      • select.interatom
      • select.read
      • select.reverse
      • select.sn_ratio
      • select.spin
      • sequence.attach_protons
      • sequence.copy
      • sequence.display
      • sequence.read
      • sequence.write
      • spectrometer.frequency
      • spectrometer.temperature
      • spectrum.baseplane_rmsd
      • spectrum.delete
      • spectrum.error_analysis
      • spectrum.error_analysis_per_field
      • spectrum.integration_points
      • spectrum.read_intensities
      • spectrum.read_spins
      • spectrum.replicated
      • spectrum.sn_ratio
      • spin.copy
      • spin.create
      • spin.create_pseudo
      • spin.delete
      • spin.display
      • spin.element
      • spin.isotope
      • spin.name
      • spin.number
      • state.load
      • state.save
      • statistics.aic
      • statistics.model
      • structure.add_atom
      • structure.add_helix
      • structure.add_model
      • structure.add_sheet
      • structure.atomic_fluctuations
      • structure.com
      • structure.connect_atom
      • structure.create_diff_tensor_pdb
      • structure.create_rotor_pdb
      • structure.create_vector_dist
      • structure.delete
      • structure.delete_ss
      • structure.displacement
      • structure.find_pivot
      • structure.get_pos
      • structure.load_spins
      • structure.mean
      • structure.pca
      • structure.read_gaussian
      • structure.read_pdb
      • structure.read_xyz
      • structure.rmsd
      • structure.rotate
      • structure.sequence_alignment
      • structure.superimpose
      • structure.translate
      • structure.web_of_motion
      • structure.write_pdb
      • system.cd
      • system.pwd
      • system.sys_info
      • system.time
      • value.copy
      • value.display
      • value.read
      • value.set
      • value.write
      • vmd.view
  • Licence
    • Copying, modification, sublicencing, and distribution of relax
    • The GPL
  
  
• Bibliography
• Index