Hi Hugh,
Welcome to the relax mailing lists! The numbers you quote don't seem
too surprising. The Dr value is very close to zero which means that
the rhombicity is very low. The Da value is hard to judge without
seeing the corresponding tm or Diso value. You could try the
following to obtain a more detailed description of the diffusion
tensor. In relax, assuming you are in the directory of the final
results file, type:
relax> state.load('results.bz2')
relax> diffusion_tensor.display()
For the ellipsoid tensor, you can directly compare the Dx, Dy, and Dz
values as these are the rotational diffusion coefficients in the three
principle directions. For the spheroid tensors, you might find the
Dratio parameter more meaningful. The display for these tensors will
also give you Dpar and Dper which are equivalent to the Dx, Dy, and Dz
eigenvalues and hence can be directly compared. Note that the purpose
of the results file is primarily to store the tensor data at full
machine precision rather than to be read (even though the information
is presented in a readable form). The diffusion_tensor.display user
function is designed to present the tensor in a more understandable
form. I hope this helps.
Regards,
Edward
On 2 February 2012 16:02, Hugh RW Dannatt <h.dannatt@xxxxxxxxxxxxxxx> wrote:
Dear All,
I have just finished fitting some relaxation data with the
full_analysis.py script, which as far I can tell has behaved exactly
as I would have expected, but I'm having trouble working out what the
numbers in the results file mean. My molecule is very anisotropic and
so the diffusion models were (with decreasing AIC) - sphere, oblate,
prolate, ellipsoid. The minimised value of Tm is also what I would
predict from the T1 & T2 values, and also matches the average number
predicted by HydroNMR. Also, the location of Rex terms correlates
nicely with what I would expect from Relaxation Dispersion studies.
Overall I'm very satisfied.
Much as the program has seemed to behave as I would expect, I am still
keen to be able to validate the results by whatever external means
possible. And so I would like to see if the degree of anisotropy fit
agrees with that predicted by HydroNMR (and, less scientifically, what
you would expect by eye!). However, the numbers in the results file
for the ellipsoid fitting seem very odd to me - I get Da = 5321992.00,
and Dr = 0.066925928). The way that they are defined in the manual
would mean that my molecule has one side several thousand times longer
than the other! In the prolate fitting I get a similar Da figure (this
time 5635770.81).
Can somebody explain to me what these numbers mean and how I can
calculate the individual anisotropic diffusion rates? If anybody has
any tips on data validation I'd be keen to hear it also.
Thanks
--
Hugh Dannatt
PhD Student Researcher
Prof. Jon Waltho Lab
Department of Molecular Biology & Biotechnology
University of Sheffield
Firth Court
Western Bank
Sheffield
S10 2TN
0114 222 2729
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Re: Anisotropic Diffusion coefficients