Hi Edward, this appears indeed to be completely unrelated to what I posted earlier.
I attached the complete script "run.py" and relaxation files containing only spin 47 to the bug report. Spin 47 alone is enough to bring relax down. I can reproduce the error with a linux machine running Suse with / without multi processor mode, and with 2.1.1 on another machine – although I will re-test that now. Some guessing (no idea, if it's relevant): It is possible, that residue 47 shows behaviour that differs from the rest of the protein. Judging from the B-factors of the included pdb file, it shows increased mobility. In the relaxation experiments however I could see residue 48 showed high R2 rates, and also having some Rex in the mf analysis (although the absolute value seems very low) - see also the attached pdf file. Cheers Martin On 04.10.2012, at 14:01, "Edward d'Auvergne" <[email protected]> wrote: > Hi Martin, > > I'm not currently able to reproduce the bug. Would you have the full > script to reproduce this? This appears to not be related to the > missing atoms in the PDB file problem you described at: > > http://thread.gmane.org/gmane.science.nmr.relax.user/1314 > http://article.gmane.org/gmane.science.nmr.relax.user/1314 > > There is no relaxation data for residues 6 and 62 in the files > attached to the bug report (https://gna.org/bugs/?20213). Have you > tried deleting other data points until you have only 2-3 residues > which still trigger the bug? To debug this, I would like to add the > absolute minimal data set and script into the relax test suite. This > should then allow me to find the bug within minutes. Without it, I am > currently a bit stuck. > > Cheers, > > Edward > > > > > On 2 October 2012 17:48, Martin Ballaschk > <[email protected]> wrote: >> URL: >> <http://gna.org/bugs/?20213> >> >> Summary: duplicate_data / deepcopy: IndexError: list >> assignment index out of range >> Project: relax >> Submitted by: mab >> Submitted on: Tue 02 Oct 2012 03:48:51 PM GMT >> Category: GUI >> Severity: 3 - Normal >> Priority: 5 - Normal >> Status: None >> Privacy: Public >> Assigned to: None >> Originator Name: >> Originator Email: >> Open/Closed: Open >> Discussion Lock: Any >> Release: 2.1.0 >> Operating System: GNU/Linux >> >> _______________________________________________________ >> >> Details: >> >> Hi Edward, >> >> during or after fitting tm, relax gives me the following error: >> >> File "/opt/relax-2.1.0/specific_fns/model_free/main.py", line 1537, in >> duplicate_data >> dp_to.mol[mol_index].res[res_index].spin[spin_index] = deepcopy(spin2) >> IndexError: list assignment index out of range >> >> The full traceback: >> >> Model-free model of spin '#1U06-H_mol1:47@N'. >> Data pipe Num_params_(k) Num_data_sets_(n) Chi2 >> Criterion >> tm0 - mf (Tue Oct 2 17:14:03 2012) 1 6 >> 1051.35716 1053.35716 >> tm1 - mf (Tue Oct 2 17:14:03 2012) 2 6 >> 28.84022 32.84022 >> tm2 - mf (Tue Oct 2 17:14:03 2012) 3 6 >> 25.50256 31.50256 >> tm3 - mf (Tue Oct 2 17:14:03 2012) 3 6 >> 3.76695 9.76695 >> tm4 - mf (Tue Oct 2 17:14:03 2012) 4 6 >> 3.76695 11.76695 >> tm5 - mf (Tue Oct 2 17:14:03 2012) 4 6 >> 25.50256 33.50256 >> tm6 - mf (Tue Oct 2 17:14:03 2012) 5 6 >> 25.50256 35.50256 >> tm7 - mf (Tue Oct 2 17:14:03 2012) 5 6 >> 3.76695 13.76695 >> tm8 - mf (Tue Oct 2 17:14:03 2012) 6 6 >> 3.76695 15.76695 >> tm9 - mf (Tue Oct 2 17:14:03 2012) 2 6 >> 683.15687 687.15687 >> The model from the data pipe 'tm3 - mf (Tue Oct 2 17:14:03 2012)' has been >> selected. >> Exception raised in thread. >> >> Traceback (most recent call last): >> File "/opt/relax-2.1.0/gui/analyses/execute.py", line 87, in run >> self.run_analysis() >> File "/opt/relax-2.1.0/gui/analyses/auto_model_free.py", line 803, in >> run_analysis >> dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, >> pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, >> diff_model=self.data.global_models, mf_models=self.data.mf_models, >> local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, >> diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, >> mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, >> conv_loop=self.data.conv_loop) >> File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 235, in >> __init__ >> self.execute() >> File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 562, in >> execute >> self.model_selection(modsel_pipe=self.name_pipe('aic'), dir=self.base_dir >> + 'aic') >> File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 769, in >> model_selection >> self.interpreter.model_selection(method='AIC', modsel_pipe=modsel_pipe, >> bundle=self.pipe_bundle, pipes=self.pipes) >> File "/opt/relax-2.1.0/prompt/uf_objects.py", line 219, in __call__ >> self._backend(*new_args, **uf_kargs) >> File "/opt/relax-2.1.0/generic_fns/model_selection.py", line 298, in select >> duplicate_data[best_model](best_model, modsel_pipe, model_info, >> global_stats=global_flag, verbose=False) >> File "/opt/relax-2.1.0/specific_fns/model_free/main.py", line 1537, in >> duplicate_data >> dp_to.mol[mol_index].res[res_index].spin[spin_index] = deepcopy(spin2) >> IndexError: list assignment index out of range >> >> The full error log is in log5.txt. >> >> I used a reduced data set of only 10 residues, still relax chokes on residue >> 47. >> >> I have no idea where this comes from. With a different crystal structure / >> pdb >> file (1shg) and relax version everything worked well and I got quite >> meaningful results. I wnated to re-run relax with another pdb structure, just >> for the heck of it. >> >> Please have a look into the "prep.py" file, that's the script I used to >> prepare the setup. >> >> I'd be very grateful if you could tell me what went wrong. >> >> The recorded data are not confidential and I could make them accessible at >> any >> time. >> >> >> >> >> _______________________________________________________ >> >> File Attachments: >> >> >> ------------------------------------------------------- >> Date: Tue 02 Oct 2012 03:48:51 PM GMT Name: log5.txt Size: 613kB By: mab >> >> <http://gna.org/bugs/download.php?file_id=16619> >> ------------------------------------------------------- >> Date: Tue 02 Oct 2012 03:48:51 PM GMT Name: prep.py Size: 3kB By: mab >> >> <http://gna.org/bugs/download.php?file_id=16620> >> >> _______________________________________________________ >> >> Reply to this item at: >> >> <http://gna.org/bugs/?20213> >> >> _______________________________________________ >> Message sent via/by Gna! >> http://gna.org/ >> >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> 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-devel
s2rex.pdf
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