Re: R2 from R1rho & R1Re: R2 from R1rho & R1Hi Edward.
I would advise not to save Rex as a value, since it is correlated with the effective field.
Ah ja, that was the problem!
Theta and the effective field are correlated (obvious).
So one can only interpolate, by determining to ramp either spin lock field or offset. I wonder how that looks as a 3D graph?
Best
Troels
Hi,
Equation 20 in that paper (http://dx.doi.org/10.1021/cr0404287) is
actually the sum of the spin-spin relaxation and Rex! This is exactly
what Troels has been working with recently. See
http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff. In the
relaxation dispersion analysis in relax we should really have two
parameters automatically generated for the user, R2 and Rex (defined
as R2 = R1rho' + Rex). These could then be used to generate
dispersion plots of R2 or Rex verses Omega_eff. This might take a
while though, in the mean time have a look at Troels' script on that
wiki page.
Regards,
Edward
On 26 March 2014 14:22, Justin Lecher <j.lecher@xxxxxxxxxxxxx> wrote:
> On 26/03/14 13:39, Edward d'Auvergne wrote:
>> Hi,
>>
>> The key here is what is meant by R2. There are many different
>> definitions. In relax, the parameter name R2 is defined as:
>>
>> - In the standard relaxation equations, spin-spin relaxation
>> component. I.e. the part influenced by the spectral density function
>> J(w).
>>
>> - Again in the standard relaxation equations, R2 is used for R2*,
>> where R2* = R2 + Rex. R2* is also defined differently if you look at
>> the exponential decay curves or if you looking at peak widths (for the
>> later there are additional factors broadening the peaks which add to
>> the R2* equation).
>>
>> - For relaxation dispersion, R2 is currently defined as R1rho', i.e.
>> just the parts influenced by the spectral density function. Here
>> R1rho' is the on-resonance part of R1rho, excluding exchange.
>>
>> R2 = R1rho' + Rex could also be defined, which is probably what you
>> are after. The value of R1rho' + Rex has been named many different
>> things by the field and there seems to be no consensus. I have
>> discussed this with Troels at
>> http://thread.gmane.org/gmane.science.nmr.relax.devel/5119/focus=5207.
>> This is a long thread with many discussions about implementing this
>> as an automatically calculated parameter - which in the end would be a
>> great feature.
>>
>> So which R2 value are you after?
>>
>> Regards,
>>
>> Edward
>
> Hi Edward,
>
> Principally I am looking for pure R2 without Rex contribution.
>
> Currently we are using some home made scripts which basically are using
> equation 20 in Palmer, Massi, 2006 (PMID 16683750).
>
>
> So for the technical side, how do I proceed in relax? Do I need to fix
> the decay for R1 and R1rho and then calculate R2 or just fit R1 and use
> my raw intensities from the R1rho measurements for the R2 calculation?
>
> Thanks,
> Justin
>
>
> --
> Justin Lecher
> Institute of Complex Systems
> ICS-6 Structural Biochemistry
> Research Centre Juelich
> 52425 Juelich, Germany
> phone: +49 2461 61 2117
>
>