Hi all
I agree with Edward about the general approach.
However, I think that when using multiple NOE sets, different spectra
(with and without saturation) shouldn't be joined together before the
analysis to permit another type of error analysis to be performed.
Hence, NOE values shouldn't be input, but the actual raw data.
Let's say you record 3 spectra with saturation and 3 spectra without
saturation. With the approach proposed before, you get 3 sets from which
you can extract errors. However, if you treat every spectrum separately,
you get 9 sets of NOEs...
1. sat-1 + nosat-1
2. sat-1 + nosat-2
3. sat-1 + nosat-3
4. sat-2 + nosat-1
5. sat-2 + nosat-2
6. sat-2 + nosat-3
7. sat-3 + nosat-1
8. sat-3 + nosat-2
9. sat-3 + nosat-3
From those 9 sets, the error calculated can be much more exact relative
to reality.
This approach has been used before in Renner et al. (JBNMR, 23 : 23-33,
2002).
Bye
Sébastien :)
Edward d'Auvergne wrote:
I think I have an idea as to how relax can be made to handle the
multiple NOE experiments (at a single field strength). The noe.read()
user function could be modified to include an argument such as
'exp_num'. The standard single NOE 'ref' and 'sat' peak intensity
list will then default to exp_num=0. The noe.error() would also
default to exp_num=0 and hence a user with a single NOE experiment
won't see any differences. This is important for compatibility
requirements between the 1.2 relax versions.
For those with multiple NOE experiments at a single field strength,
the 'exp_num' argument can be changed from 0 to 1 or higher. The rest
of the procedure will be automatic from the perspective of the user
and the NOE calculation is carried out as normal. If more than a
single experiment has been loaded into that run, the calc() user
function can determine what to do next. For the NOE value, this can
be averaged. For the NOE error two options will be possible. Firstly
if the noe.error() user function has not been invoked, then the NOE
error can be calculated from the standard deviations of a single spin
system peak intensity (with a RelaxError thrown if only two
experiments have been loaded). Secondly if errors have been set for
all loaded spectra, then the standard NOE error formula can be applied
and the error for a single spin averaged across the multiple NOE
experiments.
Does anyone see any problems with this approach? If not I'll try to
implement it soon.
Cheers,
Edward
On 3/29/07, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Hi Edward,
We currently use the second method you proposed below (calculate the
error from the deviations between peak intensities in the three
spectra). Both methods could be implemented, then the user could
choose their preferred method.
Doug
On Mar 27, 2007, at 10:11 PM, Edward d'Auvergne wrote:
Hi,
Unfortunately relax doesn't have the ability to do this but the
functionality could be added (it could even be implemented in the
relax script if all else fails). The averaging of the NOE for the
three sets is obvious, but how would you like to carry out error
analysis? Do you wish to use the RMSD of the base plane noise,
calculate three standard deviations for each spin system, and then
average that error? Do you wish to calculate the error from the
deviations between peak intensities in the three spectra? Or is there
another way to calculate the error that you would like to use?
Cheers,
Edward
On 3/28/07, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Hi All,
Does anyone have an example noe.py script to analyze and average
three identical {1H}-15N NOE experiments?
Thanks,
Doug
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______________________________________
_______________________________________________
| |
|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
|||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne |||||
|||| CREFSIP (Universite Laval, Quebec, CANADA) ||||
||| 1-418-656-2131 #4530 |||
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Re: {1H}-15N NOE analysis