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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 ===
* Start relax
* Then click: {{button|new analysis}} or {{key press|cmd|n}}
* Then click icon for {{button|R1 relaxation}} {{next}} {{button|Next}}
* Just accept name for the pipe
* Open the relax prompt: {{key press|cmd|p}}
* Paste in
<source lang="python">
import os; os.chdir(os.getenv('HOME') + os.sep + 'Desktop' + os.sep + 'Karin'); pwd()
</source>
* Then do
<source lang="python">
script(file='2_load_data.py')
</source>
* ( You can scroll through earlier commands with: {{key press|cmd|up}} )
* 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.
* {{menu|File|Save as (Shift+Ctrl+S)}} {{next}} Save as <code>before_analysis.bz2</code>
Now '''Quit relax''', and start relax again.<br>
Go to: {{menu|File|Open relax state (Ctrl+O)}} {{next}} Locate <code>before_analysis.bz2</code>
Now execute.
=== Procedure in terminal ===
The analysis can be performed by
<source lang="bash">
relax 2_load_data.py -t log.txt
</source>
== See also ==
[[Category:Tutorials]]