Hi Ed,
I got another bug... I think. The program could opened the data files for
reading, selected the model, deselected the over-fit spins, but it crashes when
starts fitting the first spin
Traceback (most recent call last):
File "/soft/group/relax/relax-1.3/relax", line 358, in ?
Relax()
File "/soft/group/relax/relax-1.3/relax", line 126, in __init__
self.interpreter.run(self.script_file)
File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 287, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, quit=self.__quit_flag, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 533, in
run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 429, in
interact_script
execfile(script_file, local)
File "full_analysis_last.py", line 197, in ?
dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
het_name=HET_NAME, relax_data=RELAX_DATA, unres=UNRES, exclude=EXCLUDE,
bond_length=BOND_LENGTH, csa=CSA, hetnuc=HETNUC, proton=PROTON,
grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_num=MC_NUM, conv_loop=CONV_LOOP)
File "/soft/group/relax/relax-1.3/auto_analyses/dauvergne_protocol.py", line
246, in __init__
self.multi_model(local_tm=True)
File "/soft/group/relax/relax-1.3/auto_analyses/dauvergne_protocol.py", line
809, in multi_model
self.interpreter.grid_search(inc=self.grid_inc)
File "/soft/group/relax/relax-1.3/prompt/minimisation.py", line 106, in
grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/soft/group/relax/relax-1.3/generic_fns/minimise.py", line 127, in
grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/soft/group/relax/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 1174, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/soft/group/relax/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 1462, in minimise
results = grid(func=self.mf.func, args=(), num_incs=inc_new,
lower=lower_new, upper=upper_new, A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
Could you take a look at this?
Thanks
Daniel
Dr. Daniel Pérez
Institut für Molekularbiologie und Biophysik
Schafmattstrasse 20
ETH-Hönggerberg, HPK G 5
CH-8093 Zürich
Phone: +41 44 633 25 37
E-mail: [email protected]
On Mar 17, 2010, at 3:02 PM, Edward d'Auvergne wrote:
> Hi,
>
> Ah, that was a real bug. I've now fixed it, so if you type 'svn up'
> in your checked out copy of relax, you will have the bug fix.
> Hopefully there won't be any more bugs hidden in there!
>
> Cheers,
>
> Edward
>
>
> 2010/3/17 Daniel Pérez <[email protected]>:
>> Hi Ed,
>>
>> Thanks for the feedback. Now dAuvergne_protocol.py is asking for defining
>> local_mf_models.
>>
>> From where should it get it? In full_analysis.py one can only define
>> local_tm_models.
>>
>>
>> With the new full_analysis I got the following:
>>
>> Traceback (most recent call last):
>> File "/soft/group/relax/relax-1.3/relax", line 358, in ?
>> Relax()
>> File "/soft/group/relax/relax-1.3/relax", line 126, in __init__
>> self.interpreter.run(self.script_file)
>> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 287, in run
>> return run_script(intro=self.__intro_string, local=locals(),
>> script_file=script_file, quit=self.__quit_flag,
>> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
>> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 533, in
>> run_script
>> return console.interact(intro, local, script_file, quit,
>> show_script=show_script, raise_relax_error=raise_relax_error)
>> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 429, in
>> interact_script
>> execfile(script_file, local)
>> File "full_analysis_last.py", line 198, in ?
>> dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
>> local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
>> het_name=HET_NAME, relax_data=RELAX_DATA, unres=UNRES, exclude=EXCLUDE,
>> bond_length=BOND_LENGTH, csa=CSA, hetnuc=HETNUC, proton=PROTON,
>> grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_num=MC_NUM, conv_loop=CONV_LOOP)
>> File "/soft/group/relax/relax-1.3/auto_analyses/dauvergne_protocol.py",
>> line 225, in __init__
>> self.status.dAuvergne_protocol.local_mf_models = local_mf_models
>> NameError: global name 'local_mf_models' is not defined
>>
>>
>> Thanks again!
>>
>> Daniel
>>
>> Dr. Daniel Pérez
>> Institut für Molekularbiologie und Biophysik
>> Schafmattstrasse 20
>> ETH-Hönggerberg, HPK G 5
>> CH-8093 Zürich
>> Phone: +41 44 633 25 37
>> E-mail: [email protected]
>>
>> On Mar 17, 2010, at 1:14 PM, Edward d'Auvergne wrote:
>>
>>> Hi,
>>>
>>> The trick here is to have a look at the new full_analysis.py sample
>>> script. This has changed quite a lot since relax-1.3.4. Most of the
>>> script has been shifted into the core of relax. Nevertheless you
>>> should be able to quite easily modify the new script to perform your
>>> analysis. There is something that will change soon with the diffusion
>>> tensor in the 1.3 repository line, so I'll tell you hopefully today
>>> how to get the change ('svn up' in the relax base directory).
>>>
>>> Regards,
>>>
>>> Edward
>>>
>>>
>>>
>>> 2010/3/17 Daniel Pérez <[email protected]>:
>>>> Hi Edward,
>>>> thanks for your quick answer.
>>>> I download the latest of relax 1.3 using
>>>>
>>>> $ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3
>>>>
>>>> Now when I run full_analysis.py with it I get the following error message
>>>>
>>>> Traceback (most recent call last):
>>>> File "/soft/group/relax/relax-1.3/relax", line 358, in ?
>>>> Relax()
>>>> File "/soft/group/relax/relax-1.3/relax", line 126, in __init__
>>>> self.interpreter.run(self.script_file)
>>>> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 287, in
>>>> run
>>>> return run_script(intro=self.__intro_string, local=locals(),
>>>> script_file=script_file, quit=self.__quit_flag,
>>>> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
>>>> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 533, in
>>>> run_script
>>>> return console.interact(intro, local, script_file, quit,
>>>> show_script=show_script, raise_relax_error=raise_relax_error)
>>>> File "/soft/group/relax/relax-1.3/prompt/interpreter.py", line 429, in
>>>> interact_script
>>>> execfile(script_file, local)
>>>> File "full_analysis.py", line 674, in ?
>>>> Main(self.relax)
>>>> AttributeError: Interpreter instance has no attribute 'relax'
>>>>
>>>>
>>>> It looks like a pretty basic error, but still I'm stacked with it
>>>> Regards
>>>> Daniel
>>>>
>>>>
>>>> Dr. Daniel Pérez
>>>> Institut für Molekularbiologie und Biophysik
>>>> Schafmattstrasse 20
>>>> ETH-Hönggerberg, HPK G 5
>>>> CH-8093 Zürich
>>>> Phone: +41 44 633 25 37
>>>> E-mail: [email protected]
>>>> Dr. Daniel Pérez
>>>> Institut für Molekularbiologie und Biophysik
>>>> Schafmattstrasse 20
>>>> ETH-Hönggerberg, HPK G 5
>>>> CH-8093 Zürich
>>>> Phone: +41 44 633 25 37
>>>> E-mail: [email protected]
>>>> On Mar 17, 2010, at 9:58 AM, Edward d'Auvergne wrote:
>>>>
>>>> Hi Daniel,
>>>>
>>>> This is actually a bug that was fixed a while ago
>>>> (http://gna.org/bugs/?15050). I have to release relax-1.3.5 soon as
>>>> there are many bug fixes in the repository sitting there waiting. If
>>>> you can't wait, you can obtain the new code by following the
>>>> instructions in one of the following:
>>>>
>>>> https://mail.gna.org/public/relax-users/2008-09/msg00002.html
>>>> https://mail.gna.org/public/relax-users/2008-10/msg00013.html
>>>> https://mail.gna.org/public/relax-users/2006-11/msg00006.html
>>>>
>>>> All the links are to help with Google indexing, just like this
>>>> http://www.nmr-relax.com/ ;) The first should be enough, but the
>>>> others might give more info if you need it.
>>>>
>>>> Regards,
>>>>
>>>> Edward
>>>>
>>>>
>>>>
>>>> 2010/3/17 Daniel Pérez <[email protected]>:
>>>>
>>>> Hi Edward,
>>>>
>>>> I hope you have some time to take a look at this. I have a data set at two
>>>> fields. I used relax for fitting the data, but when and run the
>>>> full_analysis script, after the software starts the grid search I get the
>>>> following error message
>>>>
>>>> Traceback (most recent call last):
>>>>
>>>> File "/soft/group/relax/relax-1.3.4/relax", line 418, in ?
>>>>
>>>> Relax()
>>>>
>>>> File "/soft/group/relax/relax-1.3.4/relax", line 127, in __init__
>>>>
>>>> self.interpreter.run(self.script_file)
>>>>
>>>> File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 276, in
>>>> run
>>>>
>>>> return run_script(intro=self.__intro_string, local=self.local,
>>>> script_file=script_file, quit=self.__quit_flag,
>>>> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
>>>>
>>>> File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 537, in
>>>> run_script
>>>>
>>>> return console.interact(intro, local, script_file, quit,
>>>> show_script=show_script, raise_relax_error=raise_relax_error)
>>>>
>>>> File "/soft/group/relax/relax-1.3.4/prompt/interpreter.py", line 433, in
>>>> interact_script
>>>>
>>>> execfile(script_file, local)
>>>>
>>>> File "full_analysis_markup.py", line 764, in ?
>>>>
>>>> Main(self.relax)
>>>>
>>>> File "full_analysis_markup.py", line 226, in __init__
>>>>
>>>> self.multi_model(local_tm=True)
>>>>
>>>> File "full_analysis_markup.py", line 755, in multi_model
>>>>
>>>> grid_search(inc=GRID_INC)
>>>>
>>>> File "/soft/group/relax/relax-1.3.4/prompt/minimisation.py", line 156, in
>>>> grid_search
>>>>
>>>> minimise.grid_search(lower=lower, upper=upper, inc=inc,
>>>> constraints=constraints, verbosity=verbosity)
>>>>
>>>> File "/soft/group/relax/relax-1.3.4/generic_fns/minimise.py", line 191, in
>>>> grid_search
>>>>
>>>> grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
>>>> verbosity=verbosity)
>>>>
>>>> File
>>>> "/soft/group/relax/relax-1.3.4/specific_fns/model_free/mf_minimise.py",
>>>> line
>>>> 479, in grid_search
>>>>
>>>> self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
>>>> constraints=constraints, verbosity=verbosity, sim_index=sim_index)
>>>>
>>>> File
>>>> "/soft/group/relax/relax-1.3.4/specific_fns/model_free/mf_minimise.py",
>>>> line
>>>> 789, in minimise
>>>>
>>>> model_type = self.determine_model_type()
>>>>
>>>> File "/soft/group/relax/relax-1.3.4/specific_fns/model_free/main.py", line
>>>> 1015, in determine_model_type
>>>>
>>>> if cdp.diff_tensor.fixed:
>>>>
>>>> AttributeError: 'PipeContainer' object has no attribute 'diff_tensor'
>>>>
>>>>
>>>> Checking the mailing archive I saw that Tiago Pais got the same error
>>>> message last year.
>>>>
>>>> That time you suggested him to use a script containing a markup:
>>>>
>>>> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=9794&view=markup
>>>>
>>>> (
>>>>
>>>> The complete answer was:
>>>>
>>>> Re: Error when running full_analysis.py script
>>>>
>>>> Edward d'Auvergne
>>>>
>>>> Tue, 27 Oct 2009 03:02:16 -0700
>>>>
>>>> Dear Tiago,
>>>>
>>>> This is a hard one to catch. I have just added a function to this
>>>>
>>>> script to check the validity of the user variables
>>>>
>>>> (http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=9794&view=markup).
>>>>
>>>> This should give better error messages specifically identifying the
>>>>
>>>> problem. For this second issue you are having, it is a little hard to
>>>>
>>>> see what the problem is. Would you be able to supply a little more
>>>>
>>>> information. For example the version of relax you are using, the full
>>>>
>>>> error message, how you have executed the full_analysis.py script and
>>>>
>>>> at what stage you are up to, etc. With more information, I should be
>>>>
>>>> able to track down the issue.
>>>>
>>>> Cheers,
>>>>
>>>> Edward
>>>>
>>>> )
>>>>
>>>>
>>>>
>>>> The traceback I showed to you above is coming from running that script, I
>>>> got the same error message when I run the canonical full_analysis script.
>>>>
>>>> I'm running relax 1.3.4 in RHEL distribution 5.1.19.6, kernel /vmlinuz
>>>> 2.6.18-128.1.10.e15
>>>>
>>>> It will be nice if you can help me with this
>>>>
>>>> Best regards
>>>>
>>>> Daniel
>>>>
>>>>
>>>>
>>>> Dr. Daniel Pérez
>>>>
>>>> Institut für Molekularbiologie und Biophysik
>>>>
>>>> Schafmattstrasse 20
>>>>
>>>> ETH-Hönggerberg, HPK G 5
>>>>
>>>> CH-8093 Zürich
>>>>
>>>> Phone: +41 44 633 25 37
>>>>
>>>> E-mail: [email protected]
>>>>
>>>>
>>>> _______________________________________________
>>>>
>>>> relax (http://nmr-relax.com)
>>>>
>>>> This is the relax-users mailing list
>>>>
>>>> [email protected]
>>>>
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>>>>
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>>>>
>>>> visit the list information page at
>>>>
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>>>>
>>>>
>>>>
>>
>>
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