Hi Tyler, Could you tests if it is also reproduced using the 'ellipsoid'. Since the parallel (diff_data.dpar) and perpendicular components of the diffusion tensors don't exist in the 'ellpisoid', the error might not arise, but other errors might be unmasked...
Regards, Séb Tyler Reddy wrote: > Hi Seb, > > I just tested 'oblate' and it produces the same error output. > > Tyler > > > Quoting Sébastien Morin <[EMAIL PROTECTED]>: > >> Hi Tyler, >> >> Do you get the same error when trying the 'oblate' or 'ellipsoid' >> diffusion tensors ? >> >> >> Sébastien >> >> >> Tyler Reddy wrote: >>> I'm having an issue with the full_analysis.py script. It seems to work >>> fine when >>> DIFF_MODEL = 'local_tm' or 'sphere' (converges on 4th round) but for >>> 'prolate' >>> I get the following output: >>> >>> Grid search >>> ~~~~~~~~~~~ >>> >>> Searching the grid. >>> Traceback (most recent call last): >>> File "/Applications/relax-1.3.1/relax-1.3/relax", line 408, in >>> <module> >>> Relax() >>> File "/Applications/relax-1.3.1/relax-1.3/relax", line 125, in >>> __init__ >>> self.interpreter.run(self.script_file) >>> File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>> line 270, 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_er >>> File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>> line 531, in >>> run_script >>> return console.interact(intro, local, script_file, quit, >>> show_script=show_script, raise_relax_error=raise_relax_error) >>> File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>> line 427, in >>> interact_script >>> execfile(script_file, local) >>> File "full_analysis.py", line 673, in <module> >>> Main(self.relax) >>> File "full_analysis.py", line 284, in __init__ >>> grid_search(inc=inc) >>> File "/Applications/relax-1.3.1/relax-1.3/prompt/minimisation.py", >>> line 152, >>> in grid_search >>> minimise.grid_search(lower=lower, upper=upper, inc=inc, >>> constraints=constraints, verbosity=verbosity) >>> File >>> "/Applications/relax-1.3.1/relax-1.3/generic_fns/minimise.py", line >>> 185, >>> in grid_search >>> grid_search(lower=lower, upper=upper, inc=inc, >>> constraints=constraints, >>> verbosity=verbosity) >>> File >>> "/Applications/relax-1.3.1/relax-1.3/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 >>> "/Applications/relax-1.3.1/relax-1.3/specific_fns/model_free/mf_minimise.py", >>> >>> line 987, in minimise >>> results = generic_minimise(func=self.mf.func, dfunc=self.mf.dfunc, >>> d2func=self.mf.d2func, args=(), x0=param_vector, min_algor=min_algor, >>> min_options=min_options, func_tol=func_tol, g >>> l, maxiter=max_iterations, A=A, b=b, full_output=1, >>> print_flag=verbosity) >>> File >>> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/minfx/generic.py", >>> >>> line 319, in generic_minimise >>> xk, fk, k = grid(func=func, args=args, grid_ops=min_options, >>> A=A, b=b, l=l, >>> u=u, c=c, print_flag=print_flag) >>> File >>> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/minfx/grid.py", >>> >>> line 129, in grid >>> f = func(*(params,)+args) >>> File "/Applications/relax-1.3.1/relax-1.3/maths_fns/mf.py", line >>> 506, in >>> func_diff >>> self.diff_data.calc_di(data, self.diff_data) >>> File >>> "/Applications/relax-1.3.1/relax-1.3/maths_fns/direction_cosine.py", >>> line >>> 64, in calc_spheroid_di >>> data.dz = dot(data.xh_unit_vector, diff_data.dpar) >>> TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' >>> >>> >>> >>> >>> Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: >>> >>> >>>> Hi, >>>> >>>> For the bug you mention, I've fixed this and the changes are in the >>>> repository. There were a few other issues to do with subsequent LaTeX >>>> compilation and these have been fixed too. You can see the new sample >>>> script at: http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/ >>>> >>>> Regards, >>>> >>>> Edward >>>> >>>> >>>> On Tue, Oct 21, 2008 at 3:44 AM, Tyler Reddy <[EMAIL PROTECTED]> wrote: >>>> >>>>> Hello, >>>>> >>>>> 1) I changed that line and I'm still having a bit of trouble (see >>>>> output >>>>> below). >>>>> >>>>> 2) The errors that I'm using are described as 'the standard error >>>>> for each >>>>> parameter... [which] is an easy calculation from the covariance >>>>> matrix.' >>>>> Paraphrasing from the author there--I'm guessing this isn't the >>>>> optimal >>>>> input? >>>>> >>>>> 3) I'm not sure it's explicitly stated in the manual, but I'm >>>>> proceeding on >>>>> the >>>>> assumption that you run the multi-model script first and then >>>>> modsel to >>>>> decide >>>>> on the right model for each given residue. A few weeks ago I was >>>>> experimenting >>>>> with this and if I didn't leave the global correlation time as >>>>> fixed the >>>>> computation seemed to take a VERY long time (unclear if it was >>>>> ever going to >>>>> finish). >>>>> >>>>> Also, as a side note, since my peptide is actually in a micelle, >>>>> I'm not >>>>> sure if >>>>> there's anything extra I can do for diffusion tensor and >>>>> correlation time >>>>> type >>>>> stuff. I know some programs (i.e. the Mathematica notebooks by Dr. >>>>> Spyracopoulos) read in PDB files for diffusion tensor >>>>> calculations, but I >>>>> suspect it's a bit of a mess when the system is more complicated >>>>> than the >>>>> structure in the PDB file would suggest. >>>>> >>>>> Output: >>>>> >>>>> Latex() >>>>> ---------------------------------------------------------------------------------------------------- >>>>> >>>>> >>>>> relax> pipe.create(pipe_name='results', pipe_type='mf') >>>>> >>>>> relax> results.read(file='results', dir=None) >>>>> Opening the file 'results' for reading. >>>>> Traceback (most recent call last): >>>>> File "/Applications/relax-1.3.1/relax-1.3/relax", line 408, in >>>>> <module> >>>>> Relax() >>>>> File "/Applications/relax-1.3.1/relax-1.3/relax", line 125, in >>>>> __init__ >>>>> self.interpreter.run(self.script_file) >>>>> File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>>>> line 270, >>>>> 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 "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>>>> line 531, >>>>> in >>>>> run_script >>>>> return console.interact(intro, local, script_file, quit, >>>>> show_script=show_script, raise_relax_error=raise_relax_error) >>>>> File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>>>> line 427, >>>>> in >>>>> interact_script >>>>> execfile(script_file, local) >>>>> File "latex_mf_table.py", line 220, in <module> >>>>> Latex() >>>>> File "latex_mf_table.py", line 68, in __init__ >>>>> self.table_body() >>>>> File "latex_mf_table.py", line 186, in table_body >>>>> self.file.write("%9.3f & %9.3f & " % (spin.s2, spin.s2_err)) >>>>> AttributeError: 'SpinContainer' object has no attribute 's2_err' >>>>> >>>>> >>>>> >>>>> Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: >>>>> >>>>> >>>>>> Hi, >>>>>> >>>>>> Using a new system test, I found one more bug in the script. >>>>>> This has >>>>>> been fixed in the 1.3 repository line. If you haven't used >>>>>> subversion >>>>>> to check out (and update) the 1.3 line, then you can see the changes >>>>>> required in my commit at: >>>>>> >>>>>> https://mail.gna.org/public/relax-commits/2008-10/msg00402.html >>>>>> >>>>>> Just change the line starting with '-' to the line starting with >>>>>> '+'. >>>>>> Oh, it may take a few minutes for the link to be generated. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Edward >>>>>> >>>>>> >>>>>> On Mon, Oct 20, 2008 at 10:12 PM, Edward d'Auvergne >>>>>> <[EMAIL PROTECTED]> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> That's a bug in the sample script. Try adding a ':' character >>>>>>> to the >>>>>>> end of line 171 in your script. I've fixed this in the 1.3 >>>>>>> repository >>>>>>> line and will try to add a system test to the program to try to >>>>>>> catch >>>>>>> any bugs before you do ;) >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Edward >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Mon, Oct 20, 2008 at 9:27 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote: >>>>>>> >>>>>>>> I've been trying to use the latex python script on the aic >>>>>>>> results file. >>>>>>>> I get >>>>>>>> the syntax error below. Not sure if I'm doing something wrong >>>>>>>> or if >>>>>>>> there's >>>>>>>> just a small problem with that line of code: >>>>>>>> >>>>>>>> Latex() >>>>>>>> >>>>>>>> ---------------------------------------------------------------------------------------------------- >>>>>>>> >>>>>>>> Traceback (most recent call last): >>>>>>>> File "/Applications/relax-1.3.1/relax-1.3/relax", line 408, in >>>>>>>> <module> >>>>>>>> Relax() >>>>>>>> File "/Applications/relax-1.3.1/relax-1.3/relax", line 125, in >>>>>>>> __init__ >>>>>>>> self.interpreter.run(self.script_file) >>>>>>>> File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>>>>>>> line 270, 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 "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>>>>>>> line 531, in >>>>>>>> run_script >>>>>>>> return console.interact(intro, local, script_file, quit, >>>>>>>> show_script=show_script, raise_relax_error=raise_relax_error) >>>>>>>> File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", >>>>>>>> line 427, in >>>>>>>> interact_script >>>>>>>> execfile(script_file, local) >>>>>>>> File "latex_mf_table.py", line 171 >>>>>>>> for spin, spin_id in spin_loop(return_id=True) >>>>>>>> SyntaxError: invalid syntax >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: >>>>>>>> >>>>>>>> >>>>>>>>> On Mon, Oct 20, 2008 at 5:12 PM, Tyler Reddy <[EMAIL PROTECTED]> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hello, >>>>>>>>>> >>>>>>>>>> 1) >>>>>>>>>> >>>>>>>>>> I have been using the multi model and model selection scripts in >>>>>>>>>> relax 1.3.2 but >>>>>>>>>> I have trouble displaying the output in a tabulated format. Both >>>>>>>>>> scripts seem >>>>>>>>>> to produce an xml document with various headers that isn't >>>>>>>>>> easy to >>>>>>>>>> read. It >>>>>>>>>> looks like format='columnar' isn't supported. I wonder what >>>>>>>>>> other >>>>>>>>>> options I >>>>>>>>>> have to look at this data? For some reason, I don't recall >>>>>>>>>> having >>>>>>>>>> this problem >>>>>>>>>> on a Linux machine a few weeks ago (using a Mac OS 10.4 at the >>>>>>>>>> moment), but >>>>>>>>>> anyways it would be nice to get readable model-free output. >>>>>>>>>> >>>>>>>>> The results file is now in XML format and the more readable >>>>>>>>> 'columnar' >>>>>>>>> format has been removed from the 1.3 line. With the change to >>>>>>>>> the new >>>>>>>>> XML results file all the contents of a data pipe, irrespective >>>>>>>>> of what >>>>>>>>> that data is, is packaged. So you can put data into this pipe >>>>>>>>> yourself and it will save that information (for advanced users, >>>>>>>>> complex python objects will need the to_xml() and from_xml() >>>>>>>>> methods >>>>>>>>> to package and unpackage the data). The reason for removing the >>>>>>>>> 'columnar' format was that it was considered too inflexible >>>>>>>>> for the >>>>>>>>> changes occuring in the 1.3 line, it contained duplicate >>>>>>>>> information, >>>>>>>>> had numerical precision issues, and there were alternatives to >>>>>>>>> easily >>>>>>>>> view this data. You can use the value.display() and >>>>>>>>> value.write() >>>>>>>>> user functions to display and save the results for a single >>>>>>>>> parameter. >>>>>>>>> If needed, these user functions could be extended to accept a >>>>>>>>> list of >>>>>>>>> parameters. >>>>>>>>> >>>>>>>>> Then there is the sample_scripts/latex_mf_table.py sample >>>>>>>>> script which >>>>>>>>> will generate a LaTeX table of the model-free results. This >>>>>>>>> file can >>>>>>>>> be copied and modified - this requires learning a bit of >>>>>>>>> python - to >>>>>>>>> format and display the results any way you wish. And finally if >>>>>>>>> anyone really wants to, and has the skills to, they can modify >>>>>>>>> this >>>>>>>>> sample script to recreate a version of the 'columnar' format. >>>>>>>>> This >>>>>>>>> could be added to the relax sample scripts, and if their >>>>>>>>> skills are >>>>>>>>> very advanced, then much code from the 1.2 relax versions can be >>>>>>>>> recycled. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> 2) >>>>>>>>>> >>>>>>>>>> The error input for the relaxation rate parameters is >>>>>>>>>> currently my >>>>>>>>>> non-linear >>>>>>>>>> curve fitting standard deviation. I'm not sure if that means >>>>>>>>>> subsequent >>>>>>>>>> analysis will be completely incorrect? I guess it depends on the >>>>>>>>>> comparison of >>>>>>>>>> magnitude between these errors and the type of error that is >>>>>>>>>> propagated by >>>>>>>>>> relax during its own curve-fitting (which I am unable to do >>>>>>>>>> at the >>>>>>>>>> moment). >>>>>>>>>> >>>>>>>>> I'm guessing this is the sum of squared error value (SSE) from >>>>>>>>> the >>>>>>>>> fit. Or is it a regression coefficient or a chi-squared >>>>>>>>> value? Did >>>>>>>>> the fitting use a technique such as bootstrapping or jackknife >>>>>>>>> simulations to estimate the parameter errors via propagation? >>>>>>>>> Or did >>>>>>>>> it use the covariance matrix? If it is the SSE, chi-squared, or >>>>>>>>> regression coefficient then that value cannot be used. This >>>>>>>>> will be >>>>>>>>> wildly wrong and cause massive failure in model selection. It >>>>>>>>> will >>>>>>>>> cause big problems in optimisation, and if you are unlucky and >>>>>>>>> have >>>>>>>>> spaces with long, curved valleys or flat curved spaces leading >>>>>>>>> to the >>>>>>>>> minimum (that's model-free models m5 to m8 in most cases and >>>>>>>>> not so >>>>>>>>> uncommon in model m4) then the minimum can be squeezed and >>>>>>>>> appear in >>>>>>>>> another completely different region in the space. It will >>>>>>>>> likely also >>>>>>>>> cause model failure issues, which although removed by the >>>>>>>>> eliminate() >>>>>>>>> user function, might discount the best solution. I would >>>>>>>>> guess that >>>>>>>>> all of this will have a measurable affect on the final diffusion >>>>>>>>> tensor as well and, if so, this will cause the appearance of >>>>>>>>> artificial motions (my 2007 JBNMR paper at >>>>>>>>> http://dx.doi.org/10.1039/b702202f explains these problems in >>>>>>>>> detail). >>>>>>>>> If one is not careful with the errors and they are >>>>>>>>> significantly off, >>>>>>>>> then the result is that the results may not be real. So I >>>>>>>>> would only >>>>>>>>> use the error if it comes from an established error propagation >>>>>>>>> technique (i.e. from data to parameter error propagation). >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> >>>>>>>>> Edward >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> relax (http://nmr-relax.com) >>>>>>>> >>>>>>>> This is the relax-users mailing list >>>>>>>> relax-users@gna.org >>>>>>>> >>>>>>>> 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 >>> relax-users@gna.org >>> >>> 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 >> relax-users@gna.org >> >> 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 relax-users@gna.org 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
