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The specific analyses

• 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
      • Diffusion as an ellipsoid
      • Diffusion as a spheroid
      • Diffusion as a sphere
    • The model-free models
    • Model-free optimisation theory
      • The model-free space
      • Grid search
      • Parameter constraints
      • Diagonal scaling
  • 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 ellipsoid
      • The spheroid
      • The sphere
      • The local τ_m model-free models
      • Determination of the diffusion tensor from the local τ_m parameter
    • 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
  
  
• Relaxation dispersion
  • Introduction to relaxation dispersion
    • The modelling of dispersion data
    • Implemented models
    • Dispersion model summary
      • R₁ parameter optimisation
  • The base dispersion models
    • The R2eff model
      • Fixed relaxation period experiments
      • Variable relaxation period experiments
      • Links
    • 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 SQ, ZD and DQ equations
      • The MQ equations
    • The NS MMQ 3-site linear model
      • The SQ, ZD and DQ equations
      • The MQ equations
    • The NS MMQ 3-site model
      • The SQ, ZD and DQ equations
      • The MQ equations
  • 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
  
  
• Frame order
  • Introduction of frame ordering
    • Tensors of frame ordering
    • Ln³⁺ aligned RDC and PCS data
  • Frame order theory
    • Frame order introduction
      • The ordering of a vector
      • The ordering of a frame
      • The fourth rank identity matrices
      • Tensor power of the frame order
      • The frame order motional eigenframe
      • Rotation to the average position frame of the rigid body
    • Frame order and the alignment tensor
      • The RDC and PCS
      • Alignment tensor reduction
      • The alignment tensor is the anisotropic part of a frame order matrix
    • Single pivoted motions
      • Atomic level mechanics of the single pivot
      • PCS and single pivoted motions
    • Double pivoted motions
      • Atomic level mechanics of the double pivot
      • PCS and double pivoted motions
    • Frame order in rotational Brownian diffusion and NMR relaxation
      • Free ellipsoidal Brownian diffusion
      • NMR relaxation
  • Frame order modelling
    • Rigid body motions for a two domain system
      • Ball and socket joint
      • Tilt and torsion angles from robotics
      • Model list
    • Frame order axis permutations
    • Linear constraints for the frame order models
  • Computation time and the numerical integration of the PCS
    • Numerical integration techniques
      • Monte Carlo numerical integration
      • Quasi-random numerical integration - Sobol' point sequence
      • Oversampling the Sobol' sequence points
    • Parallelization and running on a cluster
    • Frame order model nesting
      • Model categories
      • Parameter categories
      • Frame order parameter nesting in the automated protocol
    • PCS subset
    • Optimisation of the frame order models
      • Low precision grid search
      • The zooming grid search
      • The alternating grid search
      • Zooming precision optimisation
    • Error analysis
      • Low precision Monte Carlo simulations
  • The frame order data analysis
    • Introduction to frame order data analysis
    • The N-state model analysis scripts
    • The frame order analysis scripts
    • Computation times