Re: Implementation of the Schanda, Lescanne and Marion numeric dispersion model code in relax. -- July 23, 2013 - 13:06

Hi Edward,

Looks very convincing. As an alternative to Flemmings data, you might 
also just create synthetic data, by using the Bloch-McConnell equations 
to create R2eff as a function of nu_cpmg. This could, by the way, also 
be used for generating R1rho data. I don't have reference R1rho data.
paul


On 23.07.13 12:17, Edward d'Auvergne wrote:
> Hi,
>
> I forgot to mention how I validated that the numeric model code in
> relax is functional and finding the correct result.  I would have
> liked to compare the results with Flemming Hansen's CATIA program
> (http://www.biochem.ucl.ac.uk/hansen/catia/), but this relax export
> function is not implemented yet (unlike those for CMPGFit, ShereKhan,
> and NESSY).  I therefore compared the results to those of the Carver
> and Richards (CR72) analytic model using Flemming Hansen's data from
> his 2008 J. Phys. Chem. B paper (http://dx.doi.org/10.1021/jp074793o).
>   For residues 70 and 71, the analytic CR72 model results from the
> various programs and the numeric relax results are:
>
>
> The CR72 model
> ==============
>
>
> Residue :70
> -----------
>
> Param       relax       NESSY       CPMGFit     ShereKhan
> R2 (500)        7.011       7.236       6.263       7.011
> R2 (800)        9.465      10.027       6.263       9.465
> pA              0.990       0.989       0.978       0.990
> dw              5.577       5.373       0.937       5.577
> kex          1765.993    1522.059       1.774    1765.988
> chi2           18.450       7.701      65.237      18.450
>
>
> Residue :71
> -----------
>
> Param       relax       NESSY       CPMGFit     ShereKhan
> R2 (500)        4.978           -       4.983       4.978
> pA              0.997           -       0.994       0.997
> dw              4.460           -       0.757       4.461
> kex          1879.584           -       0.896    1879.618
> chi2            1.379           -       1.382       1.379
>
>
> The numeric models in relax
> ===========================
>
> Residue :70
> -----------
>
> Param     NS 2-site 3D  NS 2-site expanded   NS 2-site star
> R2 (500)         6.996               6.996            6.996
> R2 (800)         9.453               9.453            9.453
> pA               0.990               0.990            0.990
> dw               5.645               5.645            5.645
> kex           1723.443            1723.443         1723.078
> chi2            18.098              18.098           18.098
>
>
> Residue :71
> -----------
>
> Param     NS 2-site 3D  NS 2-site expanded   NS 2-site star
> R2 (500)         4.980               4.980            4.980
> pA               0.997               0.997            0.997
> dw               4.629               4.629            4.629
> kex           1805.665            1805.676         1805.110
> chi2             1.371               1.371            1.371
>
>
> This comes from the
> test_suite/shared_data/dispersion/Hansen/software_comparison file.
> For these residues, you can see that the CR72 and numeric results are
> very similar.  It could be hard to argue that they are statistically
> different.  But this shows that the code is functioning perfectly.
>
> Regards,
>
> Edward
>
>
>
> On 23 July 2013 09:28, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > Hi,
> >
> > The 2-site numeric dispersion models for CPMG data are now fully functional
> > within relax!  The following describes how these are implemented in relax
> > (to be permanently archived at
> > http://dir.gmane.org/gmane.science.nmr.relax.devel).  I hope that you will
> > check all of this by running relax and seeing for yourself.  I also have a
> > few questions below.  Note that the code is in the relax_disp branch of the
> > source code repository and that there is no official release at
> > http://www.nmr-relax.com/download.html yet.
> >
> > I have documented the numeric models now present in relax in Chapter 10 of
> > the user manual.  I have compiled the current manual for the branch and
> > uploaded it to http://download.gna.org/relax/manual/relax_disp_manual.pdf.
> > Please have a look and see what you think.  The text is extremely minimal
> > and needs to be expanded.  If you have any suggestions or additional
> > material (equations, figures, etc., and in LaTeX preferably), it would be
> > happily accepted.  For example equations for the matrices and the
> > propagation used.  The aim is to be a complete stand-alone relaxation
> > dispersion reference for the users, pointing them to all the relevant
> > literature at all possible points.  Cheers!
> >
> > As a summary, from the relax_disp.select_model user function description,
> > the numeric models are:
> >
> >      'NS 2-site 3D':  The reduced numerical solution for the 2-site
> > Bloch-McConnell equations using 3D magnetisation vectors whereby the
> > simplification R20A = R20B is assumed.  Its parameters are {R20, ..., pA,
> > dw, kex}.
> >
> >      'NS 2-site 3D full':  The full numerical solution for the 2-site
> > Bloch-McConnell equations using 3D magnetisation vectors.  Its parameters
> > are {R20A, R20B, ..., pA, dw, kex}.
> >
> >      'NS 2-site star':  The reduced numerical solution for the 2-site
> > Bloch-McConnell equations using complex conjugate matrices whereby the
> > simplification R20A = R20B is assumed.  It has the parameters {R20, ..., pA,
> > dw, kex}.
> >
> >      'NS 2-site star full':  The full numerical solution for the 2-site
> > Bloch-McConnell equations using complex conjugate matrices with parameters
> > {R20A, R20B, ..., pA, dw, kex}.
> >
> >      'NS 2-site expanded':  The numerical solution for the 2-site
> > Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov.  It
> > has the parameters {R20, ..., pA, dw, kex}.
> >
> > I would be interested to hear if you have suggestions for saner model names.
> >
> > In the auto-analysis in relax - the blackbox analysis script to make the
> > lives of users extremely easy - the *full models are not turned on by
> > default.  If curious, you can see auto-analysis script in the file
> > auto_analyses/relax_disp.py.  The auto-analysis script is normally hidden
> > from the user.  Also, please run the relax GUI with:
> >
> > $ relax --gui
> >
> > and start the relaxation dispersion analysis to see how it is implemented.
> > Note that the auto-analyses are used for the operation of all GUI analyses.
> > Using scripts, the relax user is free to do anything they wish and implement
> > any protocol they can imagine (if useful for other users, these can then be
> > converted into an auto-analysis).
> >
> > Part of the auto-analysis that I have implemented is the concept of using
> > optimised parameters from a simpler or equivalent model to speed up
> > optimisation by avoiding an expensive grid search.  For the 'full' models
> > above, I use the parameters of the simpler model and start with R20A = R20B
> > = R20.  Then, during optimisation, R20A and R20B diverge.
> >
> > For the model equivalence, this is a bit different.  I use the optimised
> > parameter values from the analytic Carver and Richards model (CR72) as the
> > starting parameters for the 'NS 2-site 3D', 'NS 2-site star' and 'NS 2-site
> > expanded' models.  This avoids the grid search and really speeds up the
> > optimisation by orders of magnitude.  It can be done because the CR72
> > results are often very similar to the numeric results.  And even a failed
> > CR72 solution is close enough to the minima to be used as a starting point
> > for the numeric models.
> >
> > I have a few other implementation questions, but I'll send these in a
> > different message for saner threads in the mailing list archives.
> >
> > Cheers,
> >
> > Edward
> >
> >
> > P. S.  Actually, I might take some of this text into the relax manual :)


--
Paul Schanda, Ph.D.
Biomolecular NMR group
Institut de Biologie Structurale Jean-Pierre Ebel (IBS)
41, rue Jules Horowitz
F-38027 Grenoble
France
+33 438 78 95 55
paul.schanda@xxxxxx
http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en