Hi,
There are three ways that an error analysis can be done for relaxation
curve fitting, although one of those is only partly implemented in
relax at the moment (that means it won't work until I write some
computer code). These are:
1. Collect all spectra in duplicate, triplicate, or more if you
really have lot of NMR time to kill, for absolutely no reason. The
peak intensity error for a single spin is calculated as the standard
deviation for each peak. Because this is inaccurate for a low replica
number, this error is averaged for all peaks to give one error per
spectrum. This error is then used in the Monte Carlo simulations.
2. If only some spectra are duplicated, then the average of the
errors for all spectra is calculated. This gives a single error value
for all spins and all spectra. This is then used in the Monte Carlo
simulations.
3. This is the error analysis technique which is not fully
implemented yet. If no spectra are recorded in duplicate, then one
needs to use the RMSD of the base plane noise. This is similar to
what relax uses for the NOE analysis (hence shouldn't be too hard to
implement for relaxation curve fitting). I would need to find the
reference, but I think this value needs to be divided or multiplied by
root 2 to convert it to a peak height uncertainty. Does anyone know a
reference for this? Then a separate error value for all spins and all
spectra can be used in the Monte Carlo simulations.
Wei Xia has recently asked the same question
(https://mail.gna.org/public/relax-users/2008-09/msg00000.html). It
might be worth reading my reply at
https://mail.gna.org/public/relax-users/2008-09/msg00002.html. So
this feature will be added to relax, but the question is how long will
that take. I'd first need the error conversion factor from RMSD of
base plane noise to peak height, and then add the ability to use the
RMSD value in relaxation curve fitting. The first part will be the
hardest, but you'll need that to do a proper Monte Carlo simulation
error analysis for the curve fitting. To do the second part I would
set up a mini analysis, lets call it a 'system test' because it tests
the system - relax - to see if the analysis works, and then make this
system test pass - i.e. implement the feature.
Don't forget that the errors in a complex analysis (e.g model-free and
reduced spectral density mapping) are just as important as the values
themselves, if not more. Getting these wrong will really damage
optimisation, model selection, and error propagation to the final
parameters via Monte Carlo simulations. So both your model-free
values and errors will be incorrect.
Regards,
Edward
On Wed, Oct 8, 2008 at 5:07 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
Hello,
It seems that Relax_fit.py requires replicate data because average
and standard
deviation values are used downstream in the analysis. With no replicate data
(since I don't have any) the output is shown below. Also, commenting out the
average and error propagation across multiple spectra
#relax_fit.mean_and_error()
doesn't work either, and I get another error output that is looking for an
averaged value. I'll probably try using a duplicate data set to
circumvent this
for now (unless this is actually another problem).
Tyler
Output:
relax> relax_fit.mean_and_error()
Calculating the average intensity and standard deviation of all spectra.
Time point: 0.01 s
Number of spectra: 1
Standard deviation for time point 0: 0.0
Time point: 0.050000000000000003 s
Number of spectra: 1
Standard deviation for time point 1: 0.0
Time point: 0.10000000000000001 s
Number of spectra: 1
Standard deviation for time point 2: 0.0
Time point: 0.20000000000000001 s
Number of spectra: 1
Standard deviation for time point 3: 0.0
Time point: 0.29999999999999999 s
Number of spectra: 1
Standard deviation for time point 4: 0.0
Time point: 0.5 s
Number of spectra: 1
Standard deviation for time point 5: 0.0
Time point: 0.80000000000000004 s
Number of spectra: 1
Standard deviation for time point 6: 0.0
Traceback (most recent call last):
File "/Applications/relax-1.3.1/relax", line 408, in <module>
Relax()
File "/Applications/relax-1.3.1/relax", line 125, in __init__
self.interpreter.run(self.script_file)
File "/Applications/relax-1.3.1/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/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/prompt/interpreter.py", line 427, in
interact_script
execfile(script_file, local)
File "relax_fit_T1_500Mhz.py", line 45, in <module>
relax_fit.mean_and_error()
File "/Applications/relax-1.3.1/prompt/relax_fit.py", line 96, in
mean_and_error
relax_fit_obj.mean_and_error()
File "/Applications/relax-1.3.1/specific_fns/relax_fit.py", line 729, in
mean_and_error
sd = sd / float(num_dups)
ZeroDivisionError: float division
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Re: Relax_fit.py problem