Hi Prem. I added the tutorial here:
http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI I tried to take power of the scripting, to get around the tedious work on defining the experiment settings for all spectra. So this script should take you to the "end point" before staring the analysis. Best Troels 2014-11-18 11:51 GMT+01:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>: > Dear Prem. > > Welcome to the mailing list! > > I guess that you mean the manual at: > http://www.nmr-relax.com/manual/Contents.html > > The relaxation dispersion auto-analysis in the GUI > > http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html > > Where the test data is in: > test_suite/shared_data/dispersion/Hansen > > I will write it up here as a script instead. > This goes a little faster testing. > > You can also find more inspiration at the wiki: > http://wiki.nmr-relax.com > http://wiki.nmr-relax.com/Category:Tutorials > > In terminal > mkdir -p $HOME/test > cd $HOME/test > gedit test.py > > Then I build the script onwards. > I run relax repeatedly, to execute code. Then I write new code in the > script, and run again. > relax test.py > > When I am satisfied, you can then do like this. > > relax -g -t log.txt > User functions -> Script -> test.py > > THEN: > 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. > > 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) > ------------------------------------------------------- > > > > > > 2014-11-18 0:06 GMT+01:00 Prem Raj Joseph <prbj123re...@gmail.com>: > > > > Hello all, > > > > I was using the GUI version of the software to run the tutorial available > > in the manual for analysis of relaxation dispersion. > > When i execute the run I get the following error > > > > RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon Nov 17 > > 10:50:08 2014)' already exists. > > > > Not sure where the error is arising from. Any help is greatly > appreciated. > > > > Thanks > > > > Prem > > > > Department of Biochemistry and Molecular Biology > > Sealy Center for Structural Biology and Molecular Biophysics > > 5.142 Medical Branch Building > > University of Texas Medical Branch > > Galveston, TX 77555-1055 > > Lab: 409-772-2181 > > Cell: 409-354-8536 > > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > Error analysis > > ============== > > > > Skipping the error analysis as it has already been performed. > > > > relax> relax_disp.r1_fit(fit=False) > > > > > > > > --------------------- > > - The 'R2eff' model - > > --------------------- > > > > > > relax> pipe.copy(pipe_from='origin - relax_disp (Mon Nov 17 10:50:08 > > 2014)', pipe_to='R2eff - relax_disp (Mon Nov 17 10:50:08 2014)', > > bundle_to='relax_disp (Mon Nov 17 10:50:08 2014)') > > Exception raised in thread. > > > > Traceback (most recent call last): > > File "/home/prem/programs/relax-3.3.2/gui/analyses/execute.py", line > 87, > > in run > > self.run_analysis() > > File "/home/prem/programs/relax-3.3.2/gui/analyses/auto_relax_disp.py", > > line 726, in run_analysis > > Relax_disp(pipe_name=self.data.pipe_name, > > pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, > > models=self.data.models, grid_inc=self.data.inc, > > mc_sim_num=self.data.mc_sim_num, exp_mc_sim_num=self.data.exp_mc_sim_num, > > pre_run_dir=self.data.pre_run_dir, > > mc_sim_all_models=self.data.mc_sim_all_models, > > insignificance=self.data.insignificance, > > numeric_only=self.data.numeric_only, r1_fit=self.data.r1_fit) > > File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py", > line > > 137, in __init__ > > self.run() > > File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py", > line > > 614, in run > > self.interpreter.pipe.copy(pipe_from=self.pipe_name, > > pipe_to=model_pipe, bundle_to=self.pipe_bundle) > > File "/home/prem/programs/relax-3.3.2/prompt/uf_objects.py", line 225, > in > > __call__ > > self._backend(*new_args, **uf_kargs) > > File "/home/prem/programs/relax-3.3.2/pipe_control/pipes.py", line 191, > > in copy > > raise RelaxPipeError(pipe_to) > > RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (Mon Nov 17 > > 10:50:08 2014)' already exists. > > _______________________________________________ > > relax (http://www.nmr-relax.com) > > > > This is the relax-users mailing list > > relax-users@gna.org > > > > To unsubscribe from this list, get a password > > reminder, or change your subscription options, > > visit the list information page at > > https://mail.gna.org/listinfo/relax-users > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
