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
>>>>>
>>>>
>>>
>>
>>
>>
>>
>
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