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
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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>
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[bug #20213] duplicate_data / deepcopy: IndexError: list assignment index out of range