Okay, I submitted the report. Let me know if there's more information you need or a better way to submit bug reports in general.. haven't done this before. Also, I had to manually copy/paste the output, and while it looks fine, if there is a problem with the same pdb structure getting read twice or something that's probably just my pasting error from the unix terminal to the browser.
On that note, how can I fix this command: relax full_analysis.py > STDOUT.txt 2> STDERR.txt tcsh: Ambiguous output redirect. Or better yet, can I merge all the output streams to a single text file and display the output in the terminal at the same time as well (maybe I'm getting too ambitious there..)? Also, I do get the same output for 'ellipsoid' as well, as Seb asked. Yours, Tyler Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: > Hi, > > This issue looks like a problem with the loaded PDB structure. The > 'local_tm' and 'sphere' optimisations do not utilise structural > information, but the 'oblate' and 'prolate' spheroids, and the > 'ellipsoid' all require this info. Normally relax will catch this > problem and deselect the spins without XH bond vectors, but this seems > to be broken in the 1.3 versions hence you get the original cryptic > Python error. As this is a real bug with the relax source code (and > not a yet-to-be converted feature or a sample script), would you be > able to submit a bug report for this issue? The relax bug tracker is > located at https://gna.org/bugs/?group=relax and the link at > https://gna.org/bugs/?func=additem&group=relax allows you to create a > report. That would be much appreciated. > > The bug report will be useful for having this error caught by the > relax test suite - if I can replicate the bug there then I can play > with the bug and fix it. Note the the actual problem occurred earlier > starting with the loading of the PDB file at the structure.read_pdb() > user function. So if you could include all print out from that user > function to the end of the traceback error message, that would be very > useful. > > Cheers, > > Edward > > > On Wed, Oct 22, 2008 at 3:17 AM, Tyler Reddy <[EMAIL PROTECTED]> 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 >>>>>>>>> [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 >>>> >>>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> > > _______________________________________________ > 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
