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__TOC__
== Tutorial ==
This follows the setup for test data in the Manual
We run relax repeatedly, to execute code. Then we write new code in the script, and run again.
When we are satisfied, one can then do like this.
Start relax
Then do
User functions -> Script -> test.py
Then a quick click on spin.isotope function, and GO.
=== The script === {{collapsible script| type = Python script| title = The test.py ===script.<source | lang="python">| script =#python 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.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
# Do for 500.
###############################################
# Change directory.
os.chdir(data + os.sep + '500_MHz')
# Get the file list, and sort the file list Alphanumericalphanumeric.
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 Readread.
spectrum.read_intensities(file=flist500, spectrum_id=ID500)
flist500rep = sort_filenames(filenames=flist500rep)
# Make ID.
ID500rep = []
for f in flist500rep: ID500rep.append("500_"+f.split(".in.bis_sparky")[0]+'b')
# Then Readread.
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 Alphanumericalphanumeric.
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 Readread.
spectrum.read_intensities(file=flist800, spectrum_id=ID800)
flist800rep = sort_filenames(filenames=flist800rep)
# Make ID.
ID800rep = []
for f in flist800rep: ID800rep.append("800_"+f.split(".in.bis_sparky")[0]+'b')
# Then Readread.
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("_")
else:
vcpmg = float(vcpmg_str.split("b")[0])
print ("%s %s %s" % (cur_id, sfrq_str, vcpmg))
# Set the current experiment type.
# 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
<source lang="bash">
cd $HOME/test/final
./grace2images.py
</source>
Go through the PNG images
Also open
<source lang="bash">
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
</source>
== Get info from log.txt ==
See [[Grep_log_file|Grep log file]] for inspiration.
Try these different grep commands
<source lang="bash">
egrep -wi --color 'relax>| model -' $HOME/test/log.txt
</source>
Find '''eliminate''' function
<source lang="bash">
egrep -wi --color -A 10 'relax> eliminate' $HOME/test/log.txt
</source>
Find '''model_selection''' function
<source lang="bash">
egrep -wi --color -A 100 'relax> model_selection' $HOME/test/log.txt
</source>