Hi Edward.
My advisor Kaare Teilum gave these references.
**********
1. Evenäs, J., Malmendal, A. & Akke, M. (2001). Dynamics of the
transition between open and closed conformations in a calmodulin
C-terminal domain mutant. Structure 9, 185–195
http://dx.doi.org/10.1016/S0969-2126(01)00575-5
2. Kempf, J.G. & Loria, J.P. (2004). Measurement of intermediate
exchange phenomena. Methods Mol. Biol. 278, 185–231
http://dx.doi.org/10.1385/1-59259-809-9:185
3. Palmer, A.G. & Massi, F. (2006). Characterization of the
dynamics of biomacromolecules using rotating-frame spin relaxation NMR
spectroscopy. Chem. Rev. 106, 1700–1719
http://dx.doi.org/10.1021/cr0404287
4. Palmer, A.G., Kroenke, C.D. & Loria, J.P. (2001). Nuclear
magnetic resonance methods for quantifying microsecond-to-millisecond
motions in biological macromolecules. Meth. Enzymol. 339,
http://dx.doi.org/10.1016/S0076-6879(01)39315-1
5. Francesca Massi, Michael J. Grey, Arthur G. Palmer III* (2005)
Microsecond timescale backbone conformational dynamics in ubiquitin
studied with NMR R1ρ relaxation experiments,
Protein science,
http://dx.doi.org/10.1110/ps.041139505
************
In general, it is the references to Palmer and Loria, which produces
these graphs.
Ref [1], Figure 1.b.
This is the bell-curves I am after, and should now be possible to
obtain, after a correction to the tilt angle calculation.
I will return with such a plot.
Ref [1], Figure 1.c.
This is the graph I am looking for.
But no clear "name" for the calculated parameter.
Ref [2], Equation 27.
Here the calculated value is noted as: R_eff. : Equation 27: R_eff =
R1rho / sin^2(theta) - R_1 / tan^2(theta) = R^{0}_2 + R_ex
Where R^{0}_2 refers to R1rho_prime as seen at http://wiki.nmr-relax.com/DPL94
Ref [3], Equation 20.
Here the calculated value is noted as: R_2: R_2 = R1rho / sin^2(theta)
- R_1 / tan^2(theta)
Figure 11+16, would be the reference.
Ref [4], Equation 43.
R_eff = R1rho / sin^2(theta) - R_1 / tan^2(theta)
Ref [5], Material and Methods, page 740.
Here the calculated value is noted as: R_2: R_2 = R^{0}_2 + R_ex.
Figure 4 would be the wished graphs.
****
A little table of conversion then gives
Relax equation | Relax store | Articles
---------------------------------------------------------------
R1rho' spin.r2 R^{0}_2 or Bar{R}_2
Fitted pars Not stored R_ex
R1rho spin.r2eff R1rho
R_1 spin.ri_data['R1'] R_1 or Bar{R}_1
The parameter is called R_2 or R_eff in the articles.
Since reff is not used in relax, this could be used?
A description could be:
* The effective rate
* The effective transverse relaxation rate constant
* The effective relaxation rate constant.
Optimal, a function: back_calc_reff
in specific_analysis.relax_disp.optimsation would be desired to enable
interpolation.
Best
Troels
2014-03-13 19:45 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi Troels,
The value of R1rho' + Rex calculated by this script, do you know if it
has a name? It is the on-resonance component of the relaxation and is
equivalent to the data from the 'R1rho - R1' type experiments. But do
you know of a base publication which gives it a name? If this
'parameter' has a name and is described in the manual, then it could
be implemented as one of the special auto-generated parameters of the
dispersion analysis. As it is, your script would function for all
dispersion models
(http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff). For some
models where the different offsets of each state is important this may
not be technically correct, but it can still be calculated.
It would be worth getting to the bottom of this. I can see that Art
Palmer sometimes plots just Rex verses w_eff. See
http://dx.doi.org/10.1110/ps.041139505. In that same publication the
parameter is defined as:
R2 = R1rho' + Rex
This is in equation 6, and is plotted in figure 4. Maybe we could
just put this equation into the manual, and add R2 as a parameter.
What do you think?
Regards,
Edward
On 13 March 2014 19:05, Troels E. Linnet
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
Follow-up Comment #32, sr #3124 (project relax):
Correct graphs of "on-resonance R1rho value with exchange" as function
"Effective field in rotating frame" finally produced manually with python
matplotlib and accessing the relax data store.
The graph is attached as:
matplotlib__52_N_R1rho_R2eff_w_eff.png
This graph corresponds to:
file #20208:
Figure2_Kjaergaard_et_al_2013_Off-resonance_R1rho_relaxation_dispersion_experiments_using_the_DPL_model.png
The production of this graph was discussed in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/5194
The R1rho_r2eff value is never calculated in relax.
This value was manually calculated by accessing the data store.
The script to produce such a graph is here:
http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff
(file #20315)
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Re: [sr #3124] Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff