Dispersion script mode - loading the data

To load the peak intensities into relax, a large data structure is first defined:

# The spectral data - spectrum ID, peak list file name, CPMG frequency (Hz), spectrometer frequency in Hertz.
data = [
    ['500_reference.in',    '500_MHz'+sep+'reference.in_sparky',           None,  500e6],
    ['500_66.667.in',       '500_MHz'+sep+'66.667.in_sparky',           66.6666,  500e6],
    ['500_133.33.in',       '500_MHz'+sep+'133.33.in_sparky',          133.3333,  500e6],
    ['500_133.33.in.bis',   '500_MHz'+sep+'133.33.in.bis_sparky',      133.3333,  500e6],
    ['500_200.in',          '500_MHz'+sep+'200.in_sparky',             200.0000,  500e6],
    ['500_266.67.in',       '500_MHz'+sep+'266.67.in_sparky',          266.6666,  500e6],
    ['500_333.33.in',       '500_MHz'+sep+'333.33.in_sparky',          333.3333,  500e6],
    ['500_400.in',          '500_MHz'+sep+'400.in_sparky',             400.0000,  500e6],
    ['500_466.67.in',       '500_MHz'+sep+'466.67.in_sparky',          466.6666,  500e6],
    ['500_533.33.in',       '500_MHz'+sep+'533.33.in_sparky',          533.3333,  500e6],
    ['500_533.33.in.bis',   '500_MHz'+sep+'533.33.in.bis_sparky',      533.3333,  500e6],
    ['500_600.in',          '500_MHz'+sep+'600.in_sparky',             600.0000,  500e6],
    ['500_666.67.in',       '500_MHz'+sep+'666.67.in_sparky',          666.6666,  500e6],
    ['500_733.33.in',       '500_MHz'+sep+'733.33.in_sparky',          733.3333,  500e6],
    ['500_800.in',          '500_MHz'+sep+'800.in_sparky',             800.0000,  500e6],
    ['500_866.67.in',       '500_MHz'+sep+'866.67.in_sparky',          866.6666,  500e6],
    ['500_933.33.in',       '500_MHz'+sep+'933.33.in_sparky',          933.3333,  500e6],
    ['500_933.33.in.bis',   '500_MHz'+sep+'933.33.in.bis_sparky',      933.3333,  500e6],
    ['500_1000.in',         '500_MHz'+sep+'1000.in_sparky',           1000.0000,  500e6],
    ['800_reference.in',    '800_MHz'+sep+'reference.in_sparky',           None,  800e6],
    ['800_66.667.in',       '800_MHz'+sep+'66.667.in_sparky',           66.6666,  800e6],
    ['800_133.33.in',       '800_MHz'+sep+'133.33.in_sparky',          133.3333,  800e6],
    ['800_133.33.in.bis',   '800_MHz'+sep+'133.33.in.bis_sparky',      133.3333,  800e6],
    ['800_200.in',          '800_MHz'+sep+'200.in_sparky',             200.0000,  800e6],
    ['800_266.67.in',       '800_MHz'+sep+'266.67.in_sparky',          266.6666,  800e6],
    ['800_333.33.in',       '800_MHz'+sep+'333.33.in_sparky',          333.3333,  800e6],
    ['800_400.in',          '800_MHz'+sep+'400.in_sparky',             400.0000,  800e6],
    ['800_466.67.in',       '800_MHz'+sep+'466.67.in_sparky',          466.6666,  800e6],
    ['800_533.33.in',       '800_MHz'+sep+'533.33.in_sparky',          533.3333,  800e6],
    ['800_533.33.in.bis',   '800_MHz'+sep+'533.33.in.bis_sparky',      533.3333,  800e6],
    ['800_600.in',          '800_MHz'+sep+'600.in_sparky',             600.0000,  800e6],
    ['800_666.67.in',       '800_MHz'+sep+'666.67.in_sparky',          666.6666,  800e6],
    ['800_733.33.in',       '800_MHz'+sep+'733.33.in_sparky',          733.3333,  800e6],
    ['800_800.in',          '800_MHz'+sep+'800.in_sparky',             800.0000,  800e6],
    ['800_866.67.in',       '800_MHz'+sep+'866.67.in_sparky',          866.6666,  800e6],
    ['800_933.33.in',       '800_MHz'+sep+'933.33.in_sparky',          933.3333,  800e6],
    ['800_933.33.in.bis',   '800_MHz'+sep+'933.33.in.bis_sparky',      933.3333,  800e6],
    ['800_1000.in',         '800_MHz'+sep+'1000.in_sparky',           1000.0000,  800e6]

In Python terminology, this is a list of lists data structure. It is essentially a matrix of information which is used in the subsequent for loop. The comment explains what each element is. For R1ρ-type experiments, the CPMG frequency column can be replaced with the spin-lock field strength. This data structure will need to be tailored to your data. It can be seen that the sep variable is now being used to specify that the Sparky files are either located in the 500_MHz or 800_MHz directories. It is used here to make this script independent of the operating system.

The Python for loop starts with the lines:

# Loop over the spectra.
for id, file, cpmg_frq, H_frq in data:

and includes all subsequently indented lines. This line of code takes the elements of the data data structure and splits it into 4 variables. Therefore for the first line, id will be set to `500_reference.in', file will be set to `500_MHz/reference.in_sparky' on a Linux machine, cpmg_frq will be None, and H_frq will be 500 MHz. For R1ρ-type data, you could change the cpmg_frq variable to field for example.

The first user function in the block loads the peak intensity data from the peak lists:

    # Load the peak intensities.
    spectrum.read_intensities(file=file, spectrum_id=id, int_method='height')

This assumes that peak heights were measured. All data will be tagged with the given ID string. For examples of peak list formats supported by relax, see Section 5.4.4 on page [*]. The next step is to specify the dispersion experiment type for each spectrum:

    # Set the relaxation dispersion experiment type.
    relax_disp.exp_type(spectrum_id=id, exp_type='SQ CPMG')

This can be `SQ CPMG', `DQ CPMG', `ZQ CPMG', `MQ CPMG', `1H SQ CPMG', `1H MQ CPMG' or `R1rho'. The next user function sets the CPMG frequencies for each spectrum:

    # Set the relaxation dispersion CPMG frequencies.
    relax_disp.cpmg_setup(spectrum_id=id, cpmg_frq=cpmg_frq)

For an R1ρ-type experiment, these lines could be changed to:

    # Set the relaxation dispersion R1rho spin lock field strength.
    relax_disp.spin_lock_field(spectrum_id=id, field=field)

Then the NMR spectrometer field strength is set:

    # Set the NMR field strength of the spectrum.
    spectrometer.frequency(id=id, frq=H_frq)

And finally the relaxation time period is set with:

    # Relaxation dispersion CPMG constant time delay T (in s).
    relax_disp.relax_time(spectrum_id=id, time=0.030)

If exponential data has been collected rather than fixed time period data, then the data data structure can have an additional column added for the relaxation times, and then this same user function can be used. The for loop will need one extra variable for the times, and this should be passed into this relax_disp.relax_time user function for the time argument.

Finally, once the for loop has completed, replicated spectra are defined with the commands:

# Specify the duplicated spectra.
spectrum.replicated(spectrum_ids=['500_133.33.in', '500_133.33.in.bis'])
spectrum.replicated(spectrum_ids=['500_533.33.in', '500_533.33.in.bis'])
spectrum.replicated(spectrum_ids=['500_933.33.in', '500_933.33.in.bis'])
spectrum.replicated(spectrum_ids=['800_133.33.in', '800_133.33.in.bis'])
spectrum.replicated(spectrum_ids=['800_533.33.in', '800_533.33.in.bis'])
spectrum.replicated(spectrum_ids=['800_933.33.in', '800_933.33.in.bis'])

The relax user manual (PDF), created 2016-10-28.