Hi Paul,
I am sending this to the relax-devel mailing to allow the discussions
to be followed by others interested in relax development, and so that
everyone including Remco knows what is happening. I have incorporated
the data from Remco Sprangers that you sent to me (and which I
attached to https://gna.org/task/?7712#comment6). The data is from:
Remco Sprangers, Anna Gribun, Peter M. Hwang, Walid A. Houry, and
Lewis E. Kay (2005) Quantitative NMR spectroscopy of supramolecular
complexes: Dynamic side pores in ClpP are important for product
release, PNAS, 102 (46), 16678-16683. (doi:
http://dx.doi.org/10.1073/pnas.0507370102)
The peak intensity and README files have been added to the
test_suite/shared_data/dispersion/Spranger_ClpP/ directory in the
relax_disp relax branch. The data will be used to test the
implementation the 'MQ NS 2-site' dispersion model (the multi-quantum
2-site numerical solution) which will soon be added to relax from the
Lescanne and Marion code attached to
https://gna.org/task/?7712#comment7.
Unfortunately I don't have enough detail to write a script to analyse
this yet. Did Remco mention for which temperature this data is for?
I would guess that this is the data shown in figure 3b. I will make
the safe assumption that residues 135 and 137 correspond to I149 and
I151 in the paper.
The mapping of CPMG frequencies of 66.7 to 1,000 Hz mentioned in the
methods section to the ncyc values of 12,1,10,2,8,3,6,4,5,1,2,3 in the
README file does not match. But assuming figure 3b, the nuCPMG values
go up to 800 Hz, which is 66.7 * 12. So I will assume 66.7 Hz (or
800/12) for one ncyc unit.
Assuming the data is from figure 3b, I will then test that relax finds
kex = 67.5 s^-1, pF = pS = 0.5, that the optimised delta_omega proton
and carbon values match those in the README file, and that R20_S and
R20_F for each residue and field are close to the plateau values in
figure 3b. I will treat the data for states S and F as separate spins
of the same residue, so that 4 independent spins are optimised with no
assumptions about their state.
The initial values for delta_omega can be used and a grid search
performed over kex, pF, and the two R20_S and R20_F parameters - and
then all parameters optimised together. This would then be equivalent
to the methods section statement "Chemical shift differences were
initially estimated from spectra recorded at 0.5°C and then optimized
based on the extracted exchange parameters from fits of the dispersion
data". Such an optimisation strategy would be only for dedicated
relax scripts and would not be present in the auto-analysis presented
in the GUI and current sample scripts. We should discuss this in a
separate thread, as you have mentioned this idea before.
Cheers,
Edward
Using Remco Sprangers' ClpP data for testing the 'MQ NS 2-site' (the multi-quantum 2-site numerical solution) relaxation dispersion model in relax.