Hi Troels,
I have seen many of these notations before. It is clear that there is
no real name for the pseudo-parameter. It looks like that R_eff was
Art's original way of denoting this and that he has now changed to R2
instead. But if you look at the reference for the TP02 dispersion
model (http://wiki.nmr-relax.com/TP02), you will see yet another
notation:
Trott, O. and Palmer, 3rd, A. G. (2002). R1rho relaxation outside
of the fast-exchange limit. J. Magn. Reson., 154(1), 157–160.
(http://dx.doi.org/10.1006/jmre.2001.2466).
Here R2 does not contain the Rex contribution. Also, Reff is absent
of Rex. But in Art's Protein Science paper, the definition R2 = R20 +
Rex is used. The MP05 model reference also does not use Reff
(http://wiki.nmr-relax.com/MP05).
For the spin.r2 parameter, this is not visible to the user (well, they
can find it if they look but it isn't presented to them) and it can
change in the future. The R1rho' value is stored there as the R20
value is also stored there, but its name can change (to r20 or r2inf
or some other joint name). In the manual you will see R1rho' and R20
listed rather than R2. I just used spin.r2 to quickly get the code
functional. The user should only see the 'r2' value if looking at the
spin container in the spin viewer window of the GUI or the XML file -
something which most will not do. Anyway, the parameter name choice
should not be based on the current variable naming.
The R_eff parameter name is confusing and it seems to have been
dropped from 2005 onwards. The R_eff name appears to be specific to
Art Palmer's group and as he himself has dropped it, then it would be
best to avoid it too. We could use 'R2'. This is not stored and can
be calculated when the user asks for it. The "R2 = R20 + Rex"
equation can be listed in the intro section of the dispersion chapter
of the manual, as well as the "R2 = R1rho / sin^2(theta)
- R_1 / tan^2(theta)" equation. The parameter description can
describe it in more detail, maybe "The effective transverse relaxation
rate with exchange, defined as R2 = R20 + Rex and R2 = R1rho /
sin^2(theta)
- R_1 / tan^2(theta)".
For the implementation, the 'back_calc' name is not quite correct, as
this is not a back-calculation but rather the direct calculation of an
auxiliary parameter. Back-calculation is the reverse of optimisation
- you go from a set of optimisable parameters back to their base data.
But the value is not optimised. It is a complicated one, but maybe
specific_analyses.relax_disp.disp_data.calc_r2() would be a better
location, to match the calc_rotating_frame_params() function?
Regards,
Edward
On 14 March 2014 14:46, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
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