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 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 > > _______________________________________________ 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
