Hi Mengjun,
Sorry for not getting back to you earlier. The papers you mention are:
Oscar Millet and Anthony Mittermaier and David Baker and Lewis E.
Kay (2003) The Effects of Mutations on Motions of Side-chains in
Protein L Studied by 2H NMR Dynamics and Scalar Couplings. Journal of
Molecular Biology, 329, 551-563
(http://dx.doi.org/10.1016/S0022-2836(03)00471-6)
Eric Johnson and Walter J. Chazin and Mark Rance (2006) Effects
of Calcium Binding on the Side-chain Methyl Dynamics of Calbindin D9k:
A 2H NMR Relaxation Study. Journal of Molecular Biology, 357,
1237-1252 (http://dx.doi.org/10.1016/j.jmb.2006.01.031).
The key here is that if these papers use the standard model-free
theory with no modifications, which I think they do though you need to
carefully check this, then this will work fine in relax where the
standard theory is implemented. If the theory has been modified and
hence is not the original equations, then it might be time to learn
some computer programming ;) But if you look at equation (1) of the
Rance paper, you will see that they measure 5 quadrupolar relaxation
rates. If you have measured these, then you cannot use them in relax
yet.
There is currently no support in relax for quadrapolar relaxation
rates. However it would be relatively easy to add. Note that all of
the required infrastructure is in place. The model-free spectral
density functions are all located in lib/spectral_densities. Also
present are all model-free models, the highest quality optimisation
infrastructure, powerful model selection techniques, model elimination
infrastructure for failed models, the automated protocol that I came
up with for solving the convoluted diffusion tensor vs. internal
motion problem (though I don't know if this protocol would work if you
only measured Me deuterium relaxation and do not combine it with
backbone relaxation), powerfully data visualisation infrastructure,
etc. The only work required is:
1) Extending the list of input relaxation data types in the
relax_data.read user function. This is trivial - the hard part is
deciding what to call these rates.
2) Adding relevant functions to the relax library
lib/auto_relaxation/ modules to handle the additional rates. This is
where the real work is.
3) Added the quadrupolar coupling constant Q (or e2qQ/h) as a
model-free parameter that can be set via the value.set user function
(see
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.parameter_object-pysrc.html#Model_free_params.__init__).
This requires one line of code.
The hardest part would be obtaining published test data. That would
only require emailing one of the corresponding authors and explaining
what you would like to do, and the data in the Rance paper, especially
figure 4 appears to be the best for this. The test data is then
turned into a system test - this is a mini-analysis used to check that
everything runs as expected. I could do this in ~2 weeks of solid
work, but I don't have the time to allocate to such a task. This
would also require the gradients and Hessians (1st and 2nd partial
derivatives) to be calculated for the relaxation rates:
http://www.nmr-relax.com/manual/Ri_theta_gradients.html
http://www.nmr-relax.com/manual/Ri_theta_Hessians.html
http://www.nmr-relax.com/manual/Ri_prime_theta_gradients.html
http://www.nmr-relax.com/manual/Ri_prime_theta_Hessians.html
This is rather trivial in Maxima, wxMaxima, Mathematica, or other
symbolic algebra systems. However it is so simple that it could be
derived by hand in a few minutes. If you would be interested in
adding this to relax, you could then mention this in your paper - that
you implemented quadrapolar relaxation rates in relax. This could
then be added to the reference list in the citations chapter
(http://www.nmr-relax.com/manual/Model_free_analysis_references.html)
as well as a new section for citations at the start of the model-free
chapter (http://www.nmr-relax.com/manual/Model_free_analysis.html) so
that people using relax with such rates should then cite your paper.
Regards,
Edward
On 12 June 2014 14:35, <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
Hi Edward,
Thank you so much. I would like to replicate the analysis in the publication
"The Effects of Mutations on Motions of Side-chains in Protein L Studied by
2H NMR Dynamics and Scalar Couplings" and "Effects of Calcium Binding on the
Side-chain Methyl Dynamics of Calbindin D9k: A 2H NMR Relaxation Study"
, where models LS2 and LS3 were used for fitting.
Best regards,
Mengjun
Quoting mengjun.xue@xxxxxxxxxxxxxxxxxxxx:
Hi Edward,
There is some script in Relax software which can be used for analyzing
side chain dynamics (R1 and R1r of deuterium in CH2D isotopomers)? Thank
you.
Best regards,
Mengjun
Re: Side chain dynamics