Hello Troels and Edwards, The modified tutorial that you sent me worked fine. Looks like I might have done some mistake while setting up the run using the original GUI tutorial for relaxation dispersion. I will try the original tutorial again to make sure the setup was fine. if the error still pops up, I will create the bug report.
Thanks again Prem On Tue, Nov 18, 2014 at 5:08 AM, Troels Emtekær Linnet < tlin...@nmr-relax.com> wrote: > 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
