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