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
