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)
>>
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>>
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>>
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>>
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