ExpSet

Experimental settings

Currently, ‘calc_rates’ supports four types of dynamics experiments: R₁ relaxation, R_1ρ relaxation (with and without magic-angle spinning), R₂, and heteronuclear NOE. To include an experiment, the ‘info’ variable must have a field corresponding to the experiment type, and that field must contain the relevant experimental information (the field may also contain information on the spin being relaxed, as discussed above). For example, to include 3 R₁ experiments, on specifies:

info.R1.v0=[400 700 1000];   %1H frequency for R1 experiments in MHz

The ‘v0’ field always specifies the magnetic field, given as the 1H frequency in MHz (‘calc_rates’ will determine the frequencies of the nucleus being relaxed), and ‘v0’ is required for all experiment types.
For R1, R2, and heteronuclear NOE experiments, the only field needed is ‘v0’, for example

info.R2.v0=[400 600];
info.NOE.v0=[750 1000];

For R_1ρ, one must also include the spin-lock strength in kHz, and may include the magic-angle spinning frequency (defaults to 0 if omitted, use for solution-state R_1ρ). For example:

info.R1p.v0=[850 850 850]; %Magnetic field
info.R1p.v1=[10 25 45]; %spin-lock strength in kHz
info.R1p.vr=[60 60 60]; %MAS frequency in kHz

One may optionally also include an offset to the spin-lock frequency:

info.R1p.off=[0 0 40];      %Spin-lock offset in kHz

Note that all fields must have the same number of elements, even if the value does not change. One additional field may be included for any of the experiment types, which gives the median standard deviation of the experiment performed (specifying the accuracy of that experiment). This is provided, with R₁ as an example, as:

info.R1.std=[.05 .12 .09];

This field is not used directly by ‘calc_rates’, but is passed in the output, and can be used for normalization of that rate constant later. In fact, this is the recommended method of normalization when using experimental data. By normalizing with the experimental standard deviation, distances between points in the resulting space will be proportional to the precision of the space. Note that for experimental data, there may be variability in the standard deviation from residue to residue, so that one first should compute the median of the standard deviation for input here.
Once all the nuclei and experiments are specified, one runs ‘calc_rates’, to obtain a structure, ‘rates’. This has the following fields:

rates.tc:   Correlation times used (same as input tc)
rates.info: Nucleus and experimental information
rates.R1:   Matrix of R1 rate constants calculated (columns: experiments, rows:
                          correlation times)
rates.R1p:  Matrix of R1rho rate constants
rates.R2:   Matrix of R2 rate constants
rates.NOE:  Matrix of NOE rate constants (this is the rate constant, not the NOE 
                          enhancement)

If a type of experiment is not included, then that field will be missing in the output.

Nuclear properties