taskrelax - Tasks: task #7800, Calculate dispersion alpha value.

 
 
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task #7800: Calculate dispersion alpha value.

Submitted by:  Troels E. Linnet <tlinnet>
Submitted on:  Tue 20 May 2014 05:31:09 PM UTC  
 
Should Start On: Tue 20 May 2014 12:00:00 AM UTCShould be Finished on: Tue 20 May 2014 12:00:00 AM UTC
Category: relax's source codePriority: 3 - Low
Status: PostponedPercent Complete: 0%
Assigned to: NoneOpen/Closed: Open
Effort: 0.00

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Tue 20 May 2014 05:31:09 PM UTC, original submission:

- Millet, O. et al. (2000) The static magnetic field dependence of
chemical exchange linebroadening defines the NMR chemical shift time
scale. J. Am. Chem. Soc., 122, 2867–2877.
(http://dx.doi.org/10.1021/ja993511y).

Specifically equation (20). This calculation could behind a user
function called relax_disp.calc_alpha. One could calculate it
directly from the optimised parameters or from the experimental R2eff
values. According to the paper:

0 <= alpha < 1 slow exchange,
alpha = 1 intermediate exchange,
1 < alpha <= 2 fast exchange.

This will help one determine if ones parameters are in the correct
exchange regime for the model one are studying. This is implemented
as part of the ShereKhan web interface, click on the [i] button next
to "Residue Selection" for details.

For testing of the CR72 model, one would require an alpha value
between 0 and 1. Fast exchange will cause the dw and pA values to
convolute and merge, so one cannot distinguish them. Hence
optimisation will look like it has failed. One can have different dw
and pA value combinations to produce the same phi_ex value, and it
will be impossible to find the original values again. That is why
there are fast exchange models with the phi_ex parameter.


The user function could be implemented as a pre-check before starting analysis.
Make a clustering or give the spins an alpha value.

Then being able to disable spins or cluster them according to the alpha value.

Troels E. Linnet <tlinnet>
Project Member

 

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    Follows 1 latest change.

    Date Changed By Updated Field Previous Value => Replaced By
    Tue 17 Jun 2014 06:33:20 PM UTCtlinnetStatusNone=>Postponed
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