Oh, was this the minfx bug that was fixed?
On Wed, Nov 5, 2008 at 9:30 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote: > I thought we already worked this one out? > > > Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: > >> Maybe this is again an edge case of an insanely difficult optimisation >> surface caused by underestimated errors. I would recommend creating a >> bug report for this. And if you could create a mini randomised data >> set which triggers this error (that could be added to the test suite >> as well), that would really help with the debugging the minfx code at >> the moment. >> >> Cheers, >> >> Edward >> >> >> On Fri, Oct 24, 2008 at 2:12 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 >>>>>>>>>>>>>>>> [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 >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >>> >>> >> >> _______________________________________________ >> 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
