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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:
<source lang="bash">
test_suite/system_tests/chemical_shift.py
test_suite/system_tests/peak_lists.py
</source>
== Run analysis in relax GUI ==
=== The Script ===
{{collapsible script
| type = relax script
| title = The <code>2_load_data.py</code> script.
| lang = python
| 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 ===
