Re: R2 from R1rho & R1 -- March 27, 2014 - 09:26

Hi Justin,

For the models you use, you need to be careful and selective.  Almost
all dispersion models are implemented in relax, but that does not mean
that they should all be used
(http://www.nmr-relax.com/manual/Dispersion_GUI_mode_choosing_models_optimise.html).
 You can think of relax as a Swiss army knife - just because scissors
are there, that does not mean you should unscrew screws with it ;)  Be
sure to read the reference paper for any model you wish to use - they
will not all be suitable for your data or your system.  Easy links to
these references can be found on the relax wiki
(http://wiki.nmr-relax.com/Category:Relaxation_dispersion).

Regards,

Edward


On 27 March 2014 08:06, Justin Lecher <j.lecher@xxxxxxxxxxxxx> wrote:
> On 26/03/14 21:35, Troels Emtekær Linnet wrote:
> > Dear 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
>
> Thanks a lot, Troels.
>
> To things I learned, first I really need to learn more on the whole
> theory and second I will try to do the full R1rho analysis and see what
> the models bring to me. I will also have a look into the Matplotlib
> script and see how it helps.
>
> Thanks,
> Justin
>
> --
> Justin Lecher
> Institute of Complex Systems
> ICS-6 Structural Biochemistry
> Research Centre Juelich
> 52425 Juelich, Germany
> phone: +49 2461 61 2117