Hi, Ah, this one is also quite commonly encountered. It's why I'm considering bundling minfx together with released versions of relax. Jack Howarth <howarth att bromo dott med dott uc dott edu> encountered the same thing (https://mail.gna.org/public/relax-users/2010-02/msg00019.html). What you have to do here is update minfx to a repository version. For this, see my response to Olivier Serve at https://mail.gna.org/public/relax-users/2009-12/msg00008.html. The problem is that the minfx API has changed, and relax was changed to match. The current version of minfx you have is not what the repository copy of relax is expecting.
Cheers, Edward 2010/3/17 Daniel Pérez <[email protected]>: > 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] >>>>> >>>>> 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 >>>>> >>>>> >>>>> >>> >>> > > _______________________________________________ relax (http://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
