Re: R2 from R1rho & R1Re: R2 from R1rho & R1Dear Justin.
If you have R1 values measured from an experiment.
And you have R1rho intensities measured as variations of spin-lock time, spin-lock offset and spin-lock field/power, you can perform R1rho analysis in relax.
If we just think of model DPL94, you would in relax get fitted R20(or R1rhoprime) and Rex (determined by fitted phi_ex, kex and calculated effective field).
Then you would like to interpolate the graph.
One could now interpolate R1rho values, by just varying theta, since we all other parameters.
The current implementation in relax is by ramping the spin-lock field, but for the graphs you refer to, it should instead ramp the offset.
I faced that exact same problem a week ago, and made this little page to show how the graph change according to that: http://wiki.nmr-relax.com/DPL94_math
So with the parameters in hand from relax, you could in a spreadsheet just vary theta and make the graphs.
But I aimed for the auto generation of these plots as grace files, and was stuck until realizing what needed to be modified in relax, since just making the graphs looked wrong.
For an implementation in relax, we need something like:
Function to ramp field values
Function to ramp offset values
Make function that return calculated R1rho data accept interpolated data
Make back calculation accept as well
Expand the grace write function
So, it takes a little before we are there. :) But now there is a plan.
Best
Troels
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