I see a similar bug that occurs right after the 'init' round. Doug
On Oct 24, 2008, at 9:52 AM, Edward d'Auvergne wrote: > Hi, > > This is a strange bug if it only occurred in the second round. I > can't see what the problem is right now so I will have to think about > this one for a bit. In the mean time, would you be able to create a > bug report for this issue? Additional information may be required to > solve this one. Again this must be specific to the system as this > code functions perfectly for other proteins, but we'll get to the > bottom of the issue. > > Cheers, > > Edward > > > On Fri, Oct 24, 2008 at 3:12 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote: >> Thanks Seb. >> >> It looks like my 'prolate' iterations in the 2nd round are maxing >> out and >> this >> is causing an error output (even though the first round seemed okay): >> >> >> k: 311 xk: array([ 2.60992216e-11, 5.00000957e+02]) >> fk: 2254.7254621187344 >> Entering sub-algorithm. >> >> Newton minimisation >> ~~~~~~~~~~~~~~~~~~~ >> Line search: Backtracking line search. >> Hessian modification: The Gill, Murray, and Wright modified >> Cholesky >> algorithm. >> >> k: 0 xk: array([ 2.60992216e-11, 5.00000957e+02]) >> fk: 2254.7254621187344 >> k: 100 xk: array([ 2.60992216e-11, 5.00000958e+02]) >> fk: 2254.7254579164155 >> k: 200 xk: array([ 2.60992216e-11, 5.00000958e+02]) >> fk: 2254.7254537140993 >> k: 300 xk: array([ 2.60992216e-11, 5.00000959e+02]) >> fk: 2254.7254495117813 >> k: 400 xk: array([ 2.60992216e-11, 5.00000959e+02]) >> fk: 2254.7254453094624 >> >> Parameter values: array([ 2.60992216e-11, 5.00000960e+02]) >> Function value: 2254.7254411071449 >> Iterations: 500 >> Function calls: 1001 >> Gradient calls: 501 >> Hessian calls: 500 >> Warning: Maximum number of iterations reached >> >> >> k: 312 xk: array([ 2.60992216e-11, 5.00000960e+02]) >> fk: 2254.7254411071449 >> Entering sub-algorithm. >> >> Newton minimisation >> ~~~~~~~~~~~~~~~~~~~ >> Line search: Backtracking line search. >> Hessian modification: The Gill, Murray, and Wright modified >> Cholesky >> algorithm. >> >> k: 0 xk: array([ 2.60992216e-11, 5.00000960e+02]) >> fk: 2254.7254411071449 >> k: 100 xk: array([ 2.60992216e-11, 5.00000961e+02]) >> fk: 2254.7254369048283 >> k: 200 xk: array([ 2.60992216e-11, 5.00000961e+02]) >> fk: 2254.7254327025107 >> k: 300 xk: array([ 2.60992216e-11, 5.00000962e+02]) >> fk: 2254.7254285001914 >> k: 400 xk: array([ 2.60992216e-11, 5.00000963e+02]) >> fk: 2254.7254242978743 >> >> Parameter values: array([ 2.60992216e-11, 5.00000963e+02]) >> Function value: 2254.7254200955554 >> Iterations: 500 >> Function calls: 1001 >> Gradient calls: 501 >> Hessian calls: 500 >> Warning: Maximum number of iterations reached >> >> >> Parameter values: array([ 2.60992216e-11, 5.00000963e+02]) >> Function value: 2254.7254200955554 >> Iterations: 156500 >> Function calls: 313313 >> Gradient calls: 156813 >> Hessian calls: 156500 >> Warning: Mu too small. >> >> >> >> Fitting to spin ':258&:[EMAIL PROTECTED]' >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> >> Method of Multipliers >> ~~~~~~~~~~~~~~~~~~~~~ >> >> k: 0 xk: array([ 0., 0.]) >> fk: 3163.7013439706825 >> Entering sub-algorithm. >> >> Newton minimisation >> ~~~~~~~~~~~~~~~~~~~ >> Line search: Backtracking line search. >> Hessian modification: The Gill, Murray, and Wright modified >> Cholesky >> algorithm. >> >> k: 0 xk: array([ 0., 0.]) >> fk: 3163.7013439706825 >> Traceback (most recent call last): >> File "/Applications/relax-1.3.1/relax-1.3/relax", line 414, in >> <module> >> Relax() >> File "/Applications/relax-1.3.1/relax-1.3/relax", line 131, 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 "full_analysis.py", line 673, in <module> >> Main(self.relax) >> File "full_analysis.py", line 300, in __init__ >> self.multi_model() >> File "full_analysis.py", line 665, in multi_model >> minimise(MIN_ALGOR) >> File "/Applications/relax-1.3.1/relax-1.3/prompt/minimisation.py", >> line >> 362, >> in minimise >> minimise.minimise(min_algor=min_algor, min_options=min_options, >> func_tol=func_tol, grad_tol=grad_tol, max_iterations=max_iterations, >> constraints=constraints, scaling=scaling, verbosity=verbosity) >> File "/Applications/relax-1.3.1/relax-1.3/generic_fns/minimise.py", >> line >> 239, >> in minimise >> minimise(min_algor=min_algor, min_options=min_options, >> func_tol=func_tol, >> grad_tol=grad_tol, max_iterations=max_iterations, >> constraints=constraints, >> scaling=scaling, verbosity=verbosity) >> 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, grad_tol=grad_tol, >> maxiter=max_iterations, A=A, b=b, full_output= >> ag=verbosity) >> File >> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ >> site-packages/minfx/generic.py", >> line 412, in generic_minimise >> results = method_of_multipliers(func=func, dfunc=dfunc, >> d2func=d2func, >> args=args, x0=x0, min_options=min_options, A=A, b=b, l=l, u=u, c=c, >> dc=dc, >> d2c=d2c, func_tol=func_tol, grad_tol=grad_tol, maxiter=maxiter, >> full_output=full_output, print_flag= >> File >> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ >> site-packages/minfx/method_of_multipliers.py", >> line 143, in method_of_multipliers >> results = min.minimise() >> File >> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ >> site-packages/minfx/method_of_multipliers.py", >> line 403, in minimise >> results = self.generic_minimise(func=self.func_LA, >> dfunc=self.func_dLA, >> d2func=self.func_d2LA, args=self.args, x0=self.xk, >> min_algor=self.min_algor, >> min_options=self.min_options, func_tol=None, grad_tol=self.tk, >> maxiter=maxiter, >> full_output=1, pr >> b_print_flag, print_prefix="\t") >> File >> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ >> site-packages/minfx/generic.py", >> line 343, in generic_minimise >> results = newton(func=func, dfunc=dfunc, d2func=d2func, args=args, >> x0=x0, >> min_options=min_options, func_tol=func_tol, grad_tol=grad_tol, >> maxiter=maxiter, >> full_output=full_output, print_flag=print_flag, >> print_prefix=print_prefix) >> File >> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ >> site-packages/minfx/newton.py", >> line 44, in newton >> results = min.minimise() >> File >> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ >> site-packages/minfx/base_classes.py", >> line 233, in minimise >> self.new_param_func() >> File >> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ >> site-packages/minfx/newton.py", >> line 166, in new_param_func >> self.line_search() >> File >> "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ >> site-packages/minfx/base_classes.py", >> line 339, in backline >> self.alpha, fc = backtrack(self.func, self.args, self.xk, self.fk, >> self.dfk, >> self.pk, a_init=self.a0) >> TypeError: 'NoneType' object is not iterable >> >> >> >> >> >> >> >> >> >> >> Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: >> >>> :S It overwrites a pre-existing file! And the important script of >>> all things!!! That'll have to be fixed. Seb, could you submit a >>> bug >>> report for that? >>> >>> Cheers, >>> >>> Edward >>> >>> >>> On Fri, Oct 24, 2008 at 2:12 PM, Sébastien Morin >>> <[EMAIL PROTECTED]> wrote: >>>> >>>> Oh... Sorry... It's still early in the morning here (Quebec >>>> City)... >>>> >>>> ... >>>> >>>> Dont' forget to specify a log file... >>>> >>>> LOG -> relax -l LOG script.py >>>> >>>> TEE -> relax -t LOG script.py >>>> >>>> If you just specify the script, the script will be erased by the >>>> log... >>>> >>>> Cheers, >>>> >>>> >>>> Séb >>>> >>>> >>>> Sébastien Morin wrote: >>>>> >>>>> Hi Tyler, >>>>> >>>>> If you want all output from relax to go to a log file, use the >>>>> option >>>>> '-l'... (relax -l script.py) >>>>> >>>>> If you want all output from relax to go to a file AND the terminal >>>>> (display), use the option '-t'... (relax -t script.py) >>>>> >>>>> These options are visible when typing : ./relax --help (or >>>>> relax -h) >>>>> >>>>> Good luck ! >>>>> >>>>> >>>>> Séb :) >>>>> >>>>> >>>>> >>>>> Tyler Reddy wrote: >>>>> >>>>>> 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 >>>>>>>>>>>>>>> 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 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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
