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 _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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