Re: Dispersion Back Calculation -- October 23, 2016 - 00:44

Hi Johns.

Look into ./test_suite/system_test/relax_disp.py

And through there find the corresponding system tests and then the data
files there, to get the structure.

For making a create data point script, that create data files upon
parameters, maybe randomize something, and then read the datafiles to read,
fit and then fit the parameters back. This is possible. I have done it
before, and in relax there is a template for 2site CPMG. But I havent done
it before 3state.

But have a look on the datastructures first.
Relax it's not geared for this kind of magic.

It's requires some knowledge first to tweak the system.

If this is something you will use repeadtly, please suggest a function that
we could create behind the scenes.


This could be of interest of interest for other scientist. ;)



Den fredag den 21. oktober 2016 skrev Jeremy Anderson <jande118@xxxxxxx>:

> Hello,
>
> I've been trying to back calculate data from parameters using the NS MMQ
> 3-site linear model.  I've tried to do something akin to the
> sample_scripts/model_free/generate_ri.py sample script as described in the
> mail-archive <http://www.mail-archive.com/relax-users@xxxxxxx/msg01783.
> html>.
> I'm afraid that I'm not knowledgable enough about the data structures,
> parameters, and functions of relax.
>
> Up to this point I have been simulating data using the CR72 and TSMFK01
> dispersion models by importing the R2eff functionality of each module into
> an ipython notebook and supplying parameters interactively.  I've attempted
> this with the NS MMQ 3-site linear model however I'm getting lost in the
> structures of the input parameters.
>
> Ideally what I would like to be able to do is input the parameters:
>
>
> pA, pB, pC = .8, .15, .05
>
> R20A, R20B, R20C = 10, 15, 20 (s^-1)
>
> dw_AB, dw_BC = 2, 2 (ppm)
>
> kex_AB, kex_BC, kex_AC = 400, 200, 0 (s^-1)
>
> dwH_AB, dwH_BC = .2, .2 (ppm)
>
>
> into the r2eff_ns_mmq_3site_mq and/or r2eff_ns_mmq_3site_sq_dq_zq functions
> of the ns_mmq_3site module and populate a back_calc array with R2eff
> values for nu_cpmg = np.logspace(1, 3, 20).  I've done the same with the
> 2-site models I mentioned above but I feel I'm a bit over my head here.
>
> Any help would be greatly appreciated and thanks in advance *and* bravo for
> all the work on relax, its great!
>
> Jeremy Anderson
>
>
>
> Ph.D. Candidate
>
> Johns Hopkins University
> Program in Molecular Biophysics
> Laboratory of Dr. Vincent J. Hilser, Ph.D.
> 3400 N Charles St, 104 Mudd Hall
> Baltimore, MD 21218
>
> (Lab) *410-516-6757*
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-- 

Troels Schwarz-Linnet