mailRe: {1H}-15N NOE analysis


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Posted by Edward d'Auvergne on March 29, 2007 - 15:47:
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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