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* test_suite/shared_data/dispersion/Hansen
→Tutorial: Formatting improvements.
__TOC__
== Tutorial ==
This follows the setup for test data in the Manual
Where the test data is in:
It is written up here as a script instead. This goes a little faster testing.
cd $HOME/test
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.<source lang="bash">relax test.py</source>When we are satisfied, one can then do like this. Start relax<source lang="bash">relax -g -t log.txt</source> 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 === {{collapsible script| type = Python script| title = The test.py script.| lang = python| script =# Python modules.import osimport globfrom 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_bundlepipe.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<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.outgedit $HOME/test/No_Rex/chi2.outgedit $HOME/test/CR72/chi2.out $HOME/test/CR72/kex.outgedit $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> == See also ==[[Category:Tutorials]][[Category:Relaxation dispersion analysis]]
