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
