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
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>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> relax (http://nmr-relax.com)
>>>>
>>>> This is the relax-users mailing list
>>>> [email protected]
>>>>
>>>> To unsubscribe from this list, get a password
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>>>>
>>>>
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>>>
>>>
>>>
>>
>>
>
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