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" <edward@xxxxxxxxxxxxx> 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 <NO-REPLY.INVALID-ADDRESS@xxxxxxx> 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 relax-devel@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-devel
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