Tutorial for R1/R2 Relaxation curve-fitting analysis from NMRView files

Data background

Based on message found at: http://thread.gmane.org/gmane.science.nmr.relax.user/1874

Data stored in several NMRView .xpk files.

relax can read the NMRView format.

• http://www.nmr-relax.com/manual/Relax_fit_script_mode_loading_the_data.html
• http://www.nmr-relax.com/manual/spectrum_read_intensities.html

The whole list of files is:

R1-methyl_hRGS4_20C_pH7_Mar2016_0ms
R1-methyl_hRGS4_20C_pH7_Mar2016_10msa
R1-methyl_hRGS4_20C_pH7_Mar2016_10msb
R1-methyl_hRGS4_20C_pH7_Mar2016_30ms
R1-methyl_hRGS4_20C_pH7_Mar2016_50ms
R1-methyl_hRGS4_20C_pH7_Mar2016_70ms
R1-methyl_hRGS4_20C_pH7_Mar2016_90msa
R1-methyl_hRGS4_20C_pH7_Mar2016_90msb
R1-methyl_hRGS4_20C_pH7_Mar2016_110ms
R1-methyl_hRGS4_20C_pH7_Mar2016_130ms
R1-methyl_hRGS4_20C_pH7_Mar2016_150ms
R1-methyl_hRGS4_20C_pH7_Mar2016_170ms
R1-methyl_hRGS4_20C_pH7_Mar2016_190ms
R1-methyl_hRGS4_20C_pH7_Mar2016_210ms
R1-methyl_hRGS4_20C_pH7_Mar2016_250ms

For determination of the errors of the intensity, there is 2x duplicated spectra (10ms, and 90ms.)

See:

• http://wiki.nmr-relax.com/Spectrum_error_analysis
• http://wiki.nmr-relax.com/RMSD

NMRView format

Each file has a structure like this:

label dataset sw sf
H1 C13
R1-methyl_hRGS4_20C_pH7_Mar2016_0ms.nv
1500.2322998 3328.125
599.802978516 150.824996948
H1.L H1.P H1.W H1.B H1.E H1.J H1.U C13.L C13.P C13.W C13.B C13.E C13.J C13.U vol int stat comment flag0
0 {75.HG11} 1.03960 0.03402 0.08416 ++ {0.0} {} {75.CG1} 21.00886 0.34258 0.60154 ++ {0.0} {} 2.09171414375 0.0213 0 {} 0
1 {75.HG21} 1.04055 0.03307 0.07450 ++ {0.0} {} {75.CG2} 20.65424 0.20240 0.50941 ++ {0.0} {} 1.69693529606 0.0198 0 {} 0
....

This is 19 Columns of data.

The first line describes what datatypes is to be found in the following lines. Here:

• Line 1 is the label of nucleus
• Line 2 is the dataset from where the file is created from
• Line 3 is the Sweep (Spectral) Width [sw] in Hz
• Line 4 is the Nuclear magnetic resonance frequency at the given spectrometer field. In MHz.

Then follow a line of header description.

• H1.L must be the label for the H1. Residue 75, atomname HG11
• Then follows .P, .W and .B
• Then follow .E, .J and .U.

Then comes for carbon C13.

Ind the end, there must be the (vol) peak volume integration intensity and the (int) the top peak point intensity.

The relax systemtests which test reading these files are found in:

test_suite/system_tests/chemical_shift.py
test_suite/system_tests/peak_lists.py

Run analysis in relax GUI

The Script

relax script: The 2_load_data.py script.

# Test if running as script or through GUI.
is_script = False
if not hasattr(cdp, "pipe_type"):
    is_script = True
    # We need to create a data pipe, which will tell relax which type of data we are expecting 
    # Taken from the relax disp manual, section 10.6.1 Dispersion script mode - the sample script
    # Create the data pipe.
    pipe_name = 'base pipe'
    pipe_bundle = 'relax_fit'
    pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_fit')


# Set path
import os
os.chdir(os.getenv('HOME') + os.sep + 'Desktop' + os.sep + 'Karin')
cwd = os.getcwd()
outdir = cwd + os.sep

NMR_freq_label = 600

files =[
['R1-methyl_hRGS4_20C_pH7_Mar2016_0ms', 0.00 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_10msa', 0.010 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_10msb', 0.010 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_30ms', 0.030 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_50ms', 0.050 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_70ms', 0.070 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_90msa', 0.090 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_90msb', 0.090 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_110ms', 0.110 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_130ms', 0.130 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_150ms', 0.150 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_170ms', 0.170 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_190ms', 0.190 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_210ms', 0.210 ],
['R1-methyl_hRGS4_20C_pH7_Mar2016_250ms', 0.250 ]]

# Delete this, when all files are there
files = files[:1]

# Create the spins from first file.
# This is to create the data containers to store the data information.
spectrum.read_spins(file="%s.xpk"%files[0][0], dir=cwd, dim=1)
spectrum.read_spins(file="%s.xpk"%files[0][0], dir=cwd, dim=2)

all_spectrum_ids = []

# Read the spectrum intensities.
for file_time in files:
    file, time = file_time
    spectrum_id = file
    all_spectrum_ids.append(spectrum_id)

    spectrum.read_intensities(file="%s.xpk"%file, dir=cwd, spectrum_id=spectrum_id, int_method='height')
    #spectrum.read_intensities(file="%s.xpk"%file, dir=cwd, spectrum_id=spectrum_id, int_method='point sum')

    # Set the relax time
    relax_fit.relax_time(time=time, spectrum_id=spectrum_id)

# Do error analysis.
# Replicated spectrums.
spectrum.replicated(spectrum_ids=['R1-methyl_hRGS4_20C_pH7_Mar2016_10msa','R1-methyl_hRGS4_20C_pH7_Mar2016_10msb'])
spectrum.replicated(spectrum_ids=['R1-methyl_hRGS4_20C_pH7_Mar2016_90msa','R1-methyl_hRGS4_20C_pH7_Mar2016_90msb'])

# Make error analysis
spectrum.error_analysis(subset=all_spectrum_ids)
#spectrum.error_analysis()

# Save the program state before run.
state.save('ini_setup', force=True)

if is_script:
#if false:
    from auto_analyses.relax_fit import Relax_fit
    GRID_INC = 21
    MC_NUM = 500
    results_directory = os.path.join(cwd, "Rx_fit")

    Relax_fit(pipe_name=pipe_name, pipe_bundle=pipe_bundle, file_root=str(NMR_freq_label), results_dir=results_directory, grid_inc=GRID_INC, mc_sim_num=MC_NUM, view_plots=False)

Procedure in GUI

• Start relax
• Then click: new analysis or ⌘ Cmd+n
• Then click icon for R1 relaxation → Next
• Just accept name for the pipe

• Open the relax prompt: ⌘ Cmd+p
• Paste in

import os; os.chdir(os.getenv('HOME') + os.sep + 'Desktop' + os.sep + 'Karin'); pwd()

• Then do

script(file='2_load_data.py')

• ( You can scroll through earlier commands with: ⌘ Cmd+↑ )
• Close the prompt window

Now save the current state! This saved state can now be loaded just before an analysis, and contain all setup and data.

• File  → Save as (Shift+Ctrl+S) → Save as before_analysis.bz2

Now Quit relax, and start relax again.
Go to: File  → Open relax state (Ctrl+O) → Locate before_analysis.bz2

Now Template:Execute

Procedure in terminal

The analysis can be performed by

relax 2_load_data.py -t log.txt