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)
>>>>
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>>>>
>>>
>>
>
>
>
>
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