Tutorial for the relaxation dispersion auto-analysis in the GUI

Tutorial

This follows the setup for test data in the Manual

• The relaxation dispersion auto-analysis in the GUI
• http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html

Where the test data is in:

test_suite/shared_data/dispersion/Hansen

It is written up here as a script instead. This goes a little faster testing.

In terminal

mkdir -p $HOME/test
cd $HOME/test
gedit test.py

Then we build the script onwards.

We run relax repeatedly, to execute code. Then we write new code in the script, and run again.

relax test.py

When we are satisfied, one can then do like this.

Start relax

relax -g -t log.txt

Then do

User functions -> Script -> test.py

THEN do:

View -> Data pipe editor -> Right click on pipe -> Associate with a new Auto analysis

This should bring you to a window, where all settings have been set.

Set

• Relaxations dispersion models: ['R2eff', 'No Rex', 'CR72', 'NS CPMG 2-site expanded']
• Grid increements: 11 (For speed-up in test phase)
• Monte-Carlo simulations number: 5 (For speed up in test phase)

Then a quick click on spin.isotope function, and GO.

The script

Python script: The test.py script.

# Python modules.
import os
import glob
from time import asctime, localtime

# relax modules.
from lib.io import sort_filenames

# Set path to data.
data = '/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/shared_data/dispersion/Hansen'

# Create the data pipe.
pipe_bundle = "relax_disp (%s)" % asctime(localtime())
pipe_name = "origin - %s" % pipe_bundle
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')

# Create spin to hold data.
sequence.read(file='fake_sequence.in', dir=data, res_num_col=1, res_name_col=2)
deselect.read(file='unresolved', dir=data+os.sep+'500_MHz', spin_id_col=None, mol_name_col=None, res_num_col=1, boolean='AND', change_all=False)
deselect.read(file='unresolved', dir=data+os.sep+'800_MHz', spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, boolean='AND', change_all=False)

# Give the spins attributes.
spin.isotope(isotope='15N', spin_id='@*', force=True)
spin.name(name='N')

# Do for 500.
#############

# Change directory.
os.chdir(data + os.sep + '500_MHz')

# Get the file list, and sort the file list alphanumeric.
flist500 = glob.glob('*.in_sparky')
flist500 = sort_filenames(filenames=flist500)

# Make ID.
ID500 = []
for f in flist500: ID500.append("500_"+f.split(".in_sparky")[0])

# Then read.
spectrum.read_intensities(file=flist500, spectrum_id=ID500)

# Repeat for the replicated spectra.
flist500rep = glob.glob('*in.bis_sparky')
flist500rep = sort_filenames(filenames=flist500rep)

# Make ID.
ID500rep = []
for f in flist500rep: ID500rep.append("500_"+f.split(".in.bis_sparky")[0]+'b')

# Then read.
spectrum.read_intensities(file=flist500rep, spectrum_id=ID500rep)

# Then map replicated.
for b_id in ID500rep:
    a_id = b_id[:-1]
    spectrum.replicated(spectrum_ids=[a_id, b_id])

# Then check.
print(cdp.replicates)

# Then repeat for 800.
######################

# Change directory.
os.chdir(data + os.sep + '800_MHz')

# Get the file list, and sort the file list alphanumeric.
flist800 = glob.glob('*.in_sparky')
flist800 = sort_filenames(filenames=flist800)

# Make ID.
ID800 = []
for f in flist800: ID800.append("800_"+f.split(".in_sparky")[0])

# Then read.
spectrum.read_intensities(file=flist800, spectrum_id=ID800)

# Repeat for the replicated spectra.
flist800rep = glob.glob('*in.bis_sparky')
flist800rep = sort_filenames(filenames=flist800rep)

# Make ID.
ID800rep = []
for f in flist800rep: ID800rep.append("800_"+f.split(".in.bis_sparky")[0]+'b')

# Then read.
spectrum.read_intensities(file=flist800rep, spectrum_id=ID800rep)

# Then map replicated.
for b_id in ID800rep:
    a_id = b_id[:-1]
    spectrum.replicated(spectrum_ids=[a_id, b_id])

# Then check.
print(cdp.replicates)
print("%s %s %s %s" % (len(ID500), len(ID500rep), len(ID800), len(ID800rep)))

# Then set spectrum properties.
all_ID = ID500 + ID500rep + ID800 + ID800rep

for cur_id in all_ID:
    # Split from name.
    sfrq_str, vcpmg_str = cur_id.split("_")

    if vcpmg_str == 'reference':
         vcpmg = None
    else:
        vcpmg = float(vcpmg_str.split("b")[0])
    print("%s %s %s" %  (cur_id, sfrq_str, vcpmg))

    # Set the current experiment type.
    relax_disp.exp_type(spectrum_id=cur_id, exp_type='SQ CPMG')

    # Set the NMR field strength of the spectrum.
    spectrometer.frequency(id=cur_id, frq=float(sfrq_str), units='MHz')

    # Relaxation dispersion CPMG constant time delay T (in s).
    relax_disp.relax_time(spectrum_id=cur_id, time=0.03)

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

Inspect results

Go to the final folder.

Execute

cd $HOME/test/final
./grace2images.py

Go through the PNG images

Also open

gedit $HOME/test/log.txt $HOME/test/final/chi2.out $HOME/test/final/models.out
gedit $HOME/test/No_Rex/chi2.out
gedit $HOME/test/CR72/chi2.out $HOME/test/CR72/kex.out
gedit $HOME/test/NS_CPMG_2-site_expanded/chi2.out $HOME/test/NS_CPMG_2-site_expanded/kex.out

Get info from log.txt

See Grep log file for inspiration.

Try these different grep commands

egrep -wi --color 'relax>| model -' $HOME/test/log.txt

Find eliminate function

egrep -wi --color -A 10 'relax> eliminate' $HOME/test/log.txt

Find model_selection function

egrep -wi --color -A 100 'relax> model_selection' $HOME/test/log.txt