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
>>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
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>>
>
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