Hi, It may be due to single field strength data, but I would guess that it is some other problem. If it reappears when you are analysing your data in another way, then I'll instantly fix it. This will require a bug report with truncated data so that I can replicate the bug, then it usually takes me ~5 min to fix, otherwise it will take much longer for me to find the site of the problem. I have talked in detail about the issue of single field strength data before. Rather than repeating everything again, I would recommend you to read my post at https://mail.gna.org/public/relax-users/2008-03/msg00004.html. The first 2 paragraphs are all that are relevant. I hope this helps.
Regards, Edward 2009/10/28 Tiago Pais <[email protected]>: > 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
