Hello Edward, I tried the GUI version of the setup again for the relaxation dispersion (on the test data) and it ran without any error this time. Its possible I made some mistake during the setup thr last time.
Thank again for the help Prem On Tue, Nov 18, 2014 at 5:27 AM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi Troels and Prem, > > Troels, for a suggestion for improving the script in your tutorial, > you could use: > > """ > from time import asctime, localtime > > pipe_bundle = "relax_disp (%s)" % asctime(localtime()) > pipe_name = "origin - %s" % pipe_bundle > """ > > This is how the new analysis wizard in relax creates these names > ( > http://www.nmr-relax.com/api/3.3/gui.analyses.wizard-pysrc.html#Data_pipe_page.on_display > ). > This script really saves a lot of time. But, as it does not replicate > the bug, Prem, could you still create the bug report and include all > steps required to produce the error you observed? > > Cheers, > > Edward > > > > On 18 November 2014 12:08, 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 > _______________________________________________ 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
