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
