Hi Edward, thank you for looking into this. Of course you may include the data in the test suite.
Cheers Martin On 04.10.2012, at 18:05, "Edward d'Auvergne" <[email protected]> wrote: > Hi, > > For attachments, could I ask you to avoid sending them to public > mailing lists? This causes significant strain on the infrastructure. > It is better for reference to attach it to a relevant bug/support/task > report. > > I can now reproduce the problem and see what the issue is. If it is > ok, I will add your data in the files 'sh3-47.2.zip' and 'run.py' > (attached to https://gna.org/bugs/?20213) to the relax test suite so > that this bug will never be able to return to relax. I can speed this > up for the test suite by only using model 'tm0', using 2 grid search > increments, and only having residue 47 in the PDB file. The issue is > because of the following user function (with output): > > relax> structure.load_spins(spin_id='@N*', ave_pos=True) > Adding the following spins to the relax data store. > > # mol_name res_num res_name spin_num spin_name > 1U06-H_mol1 47 ASN 350 N > 1U06-H_mol1 47 ASN 360 ND2 > 1U06-H_mol1 47 ASN 361 ND2 > > This should in reality not be a problem - relax should handle this. > But a workaround which does not trigger the bug is to load only the > backbone nitrogens with: > > structure.load_spins(spin_id='@N', ave_pos=True) > > You will see this in the sample script for relax 2.1.1. I will work > on this bug, but the temporary solution is to not load the Asn and Gln > sidechain nitrogens. Loading the Trp sidechain is however ok. > > Cheers, > > Edward > > > > > On 4 October 2012 15:27, Martin Ballaschk <[email protected]> wrote: >> 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 o>>>> 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>>>> 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 >> >> _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users 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-users
