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Tutorial for the relaxation dispersion auto-analysis in the GUI

4,381 bytes added, 11:02, 18 November 2014

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gedit test.py

</source>

Then we build the script onwards.<br>

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.

=== test.py ===

#python modules

import os

import glob

# 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_name = 'origin - relax_disp (Tue Nov 18 10:39:36 2014)'

pipe_bundle = 'relax_disp (Tue Nov 18 10:39:36 2014)'

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 800.

###############################################

# 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 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 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)

</source>

== See also ==

[[Category:Tutorials]]

[[Category:Relaxation dispersion analysis]]

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