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 <edward@xxxxxxxxxxxxx> 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 <tlinnet@xxxxxxxxxxxxx> wrote:Hi Prem. I added the tutorial here:http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUII 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 <tlinnet@xxxxxxxxxxxxx :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 GUIhttp://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.htmlWhere 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 CPMG2-siteexpanded'] 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 <prbj123relax@xxxxxxxxx>:Hello all, I was using the GUI version of the software to run the tutorialavailablein 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 (MonNov 1710:50:08 2014)' already exists. Not sure where the error is arising from. Any help is greatlyappreciated.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", line87,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",line137, in __init__ self.run() File "/home/prem/programs/relax-3.3.2/auto_analyses/relax_disp.py",line614, 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", line225,in__call__ self._backend(*new_args, **uf_kargs) File "/home/prem/programs/relax-3.3.2/pipe_control/pipes.py", line191,in copy raise RelaxPipeError(pipe_to) RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp (MonNov 1710:50:08 2014)' already exists. _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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@xxxxxxx 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