I find no evidence of a problem related to data not loaded. On the other hand I didn't notice the information at the beginning of the script stating that "multiple magnetic field strength" data was essential. Do you think this might be really the problem? How can I solve it? I have data acquired only at one field strength. Is there another sample script more suitable? Best regards TiagoP
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 28 de Outubro de 2009 12:50 To: Tiago Pais Cc: [email protected] Subject: Re: Error when running full_analysis.py script Hi, I'm not exactly sure what the problem is, but I would get that there is a warning thrown when loading the relaxation data that no data was loaded? This error has been encountered before, but I thought it had been fixed. Another issue is that your are using single field strength data, but in the introduction for this script it says: "Importantly data at multiple magnetic field strengths is essential for this analysis." I've now added a check for this to the script (available from the download link at http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=983 4&view=markup). Cheers, Edward 2009/10/27 Tiago Pais <[email protected]>: > Sorry, forgot to attach the script. > TP > > -----Original Message----- > From: Tiago Pais [mailto:[email protected]] > Sent: terça-feira, 27 de Outubro de 2009 12:17 > To: 'Edward d'Auvergne' > Cc: 'Sébastien Morin'; 'Boaz Shapira'; '[email protected]' > Subject: RE: Error when running full_analysis.py script > > Dear Edward, > I will try to provid the most complete information since I have not managed > to solve the problem yet: > > 1- Relax version 1.3.4 running under Ubuntu 9.04 virtual machine > 2- I have executed the script in the command line by typing "relax > full_analysis.py". The location is /home/tpais/ModelFree/PHS/teste/ > 3- I am in the initial steps of the script with the diffusion model set to > "local_tm". > 4-the script still manages to run for a couple of minutes executing some > Newton minimizations and still writes 4 files (tm0, tm1,...) within the > subdirectory "/local_tm". These are the last lines showing up before the > error occurs: > "File "full_analysis.py", line 220, in __init__ > self.multi_model(local_tm=True) > File "full_analysis.py", line 662, in multi_model > grid_search(inc=GRID_INC) > File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_search > minimise.grid_search(lower=lower, upper=upper, inc=inc, > constraints=constraints, verbosity=verbosity) > File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_search > grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints, > verbosity=verbosity) > File "/usr/local/relax/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 "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 789, > in minimise > model_type = self.determine_model_type() > File "/usr/local/relax/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'" > > > 5- I also send attached the script as I am using it. > > By the way, I tried to run the script with the new function and it gave an > indentation error ("IndentationError: expected an indented block") probably > because I copy/past it directly from the link you provided) > > Regards, > TiagoP > > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Edward d'Auvergne > Sent: terça-feira, 27 de Outubro de 2009 10:02 > To: Tiago Pais > Cc: Sébastien Morin; Boaz Shapira; [email protected] > Subject: Re: Error when running full_analysis.py script > > 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=97 > 94&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 > > > > 2009/10/22 Tiago Pais <[email protected]>: >> Hi Sebastien, >> The thing is it was not exactly an error of the script. In the line 639 > you >> have to adjust the script so that it agrees with the format of the > function >> that you have used in line 174 "Relax_Data=[...". If in line 174 you >> describe the data sets with only three parameters (e.g.[Rilabel, freq, >> file]) then, in line 639 you have to adapt the function so that the > program >> reads only three sets of parameters (e.g. relax_data.read(data[0], > data[1], >> data[2], data[3]) while in the original file was set to read 13. >> This is beginners' stuff, but that's exactly what I am with respect to > RELAX >> and PYTHON, so it may be usefull for other beginners. >> >> However, I still have not managed to run the script to the end. At the >> moment I am stuck with yet another error message: AttributeError: >> 'PipeContainer' object has no attribute 'diff_tensor' >> >> If anyone can help me and avoid that I loose time with this probably easy > to >> solve error, please do. >> Thanks >> Tiago P >> >> -----Original Message----- >> From: Sébastien Morin [mailto:[email protected]] >> Sent: quarta-feira, 21 de Outubro de 2009 19:46 >> To: Tiago Pais >> Cc: 'Edward d'Auvergne'; 'Boaz Shapira'; [email protected] >> Subject: Re: Error when running full_analysis.py script >> >> Dear Tiago, >> >> Just for the logs, could you tell us what was the problem ? >> >> Regards, >> >> >> Sébastien >> >> >> Tiago Pais wrote: >>> Ok, managed to solve this already. >>> Cheers >>> Tiago >>> >>> -----Original Message----- >>> From: [email protected] [mailto:[email protected]] On >>> Behalf Of Tiago Pais >>> Sent: quarta-feira, 21 de Outubro de 2009 15:53 >>> To: 'Edward d'Auvergne'; 'Boaz Shapira' >>> Cc: [email protected] >>> Subject: Error when running full_analysis.py script >>> >>> Dear all, >>> I am using 15N relaxation data previously analyzed to test some of the >>> scripts available in Relax to make sure that I am using it correctly. >>> However, I get the following error message when running the sample script >>> full_analysis.py: "List Index out of Range" >>> Below is "print screen" where the error shows up at the bottom: >>> >>> "None 149 Q None None >>> >>> relax> spin.name(spin_id=None, name='N', force=False) >>> Traceback (most recent call last): >>> File "/usr/local/bin/relax", line 418, in <module> >>> Relax() >>> File "/usr/local/bin/relax", line 127, in __init__ >>> self.interpreter.run(self.script_file) >>> File "/usr/local/relax/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 "/usr/local/relax/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 "/usr/local/relax/prompt/interpreter.py", line 433, in >>> interact_script >>> execfile(script_file, local) >>> File "full_analysis.py", line 671, in <module> >>> Main(self.relax) >>> File "full_analysis.py", line 220, in __init__ >>> self.multi_model(local_tm=True) >>> File "full_analysis.py", line 639, in multi_model >>> relax_data.read(data[0], data[1], data[2], data[3], data[4], data[5], >>> data[6], data[7], data[8], data[9], data[10], data[11], >>> data[12]) >>> IndexError: list index out of range" >>> >>> I can't understand if the error relates to the last command listed, >> actually >>> I can't understand the command given in this line (639) - what is it >> suppose >>> to do? >>> >>> Best regards >>> TiagoP >>> >>> >>> _______________________________________________ >>> 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 >>> >> >> >> -- >> Sébastien Morin >> PhD Student >> S. Gagné NMR Laboratory >> Université Laval & PROTEO >> Québec, Canada >> >> > > _______________________________________________ > 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
