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" <edward@xxxxxxxxxxxxx>
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 <ballaschk@xxxxxxxxxxxxx>
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" <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 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>
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Re: [bug #20213] duplicate_data / deepcopy: IndexError: list assignment index out of range