URL: <http://gna.org/task/?7800> Summary: Calculate dispersion alpha value. Project: relax Submitted by: tlinnet Submitted on: Tue 20 May 2014 05:31:09 PM UTC Should Start On: Tue 20 May 2014 12:00:00 AM UTC Should be Finished on: Tue 20 May 2014 12:00:00 AM UTC Category: relax's source code Priority: 3 - Low Status: None Percent Complete: 0% Assigned to: None Open/Closed: Open Discussion Lock: Any Effort: 0.00 _______________________________________________________ Details: - 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. _______________________________________________________ Reply to this item at: <http://gna.org/task/?7800> _______________________________________________ Message sent via/by Gna! http://gna.org/