URL: <http://gna.org/support/?3154> Summary: Implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales Project: relax Submitted by: tlinnet Submitted on: Tue 29 Apr 2014 10:25:52 PM UTC Category: Feature request Priority: 5 - Normal Severity: 3 - Normal Status: None Assigned to: tlinnet Originator Email: Open/Closed: Open Discussion Lock: Any Operating System: None _______________________________________________________ Details: This is a feature request for the implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales. http://dx.doi.org/10.1016/j.jmr.2014.02.023 "An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange" Andrew J. Baldwin Journal of Magnetic Resonance Main feature: In practise, significant deviations from the Carver Richards equation can be incurred if pB>1%. Incorporation of the correction term into equation (article equation 50), results in an improved description of the CPMG experiment over the Carver Richards equation. ################################################## ##### Comments from the Author, revised by Troels. The formula is quite similar to the Carver Richards, so it'll be a bit slower. It terms of raw speed, I've found it about 100 times faster than a numerical solution, and about 3x slower than Carver Richards. That fits roughly with the number of extra function calls. Note that using arc-cos, rather than square roots to get the prefactors for the Eigenvalues in the first few lines speeds things up a little. This little timesaver would work also in your implementation of the Carver Richard's formula. The advantage of this code will be that you'll always get the right answer provided you've got 2-site exchange, in-phase magnetisation and on-resonance pulses. With Mieboom and Carver Richard's equations, on occasion, you'll get the wrong answer (in this scenario). I wonder why it would ever make sense to use either of these? If you ever saw a better fit when using either, in terms of chi2, it would be fake, as they all reduce into each other, so the limiting cases are utterly redundant? Following on from that, given that in any real experiment (apart from the rare case where you explicit decouple during the CPMG period) you'll have elements of scalar coupling, pulses will rarely be on-resonance and you'll have additional relaxation effects like spin-flips. So what is the benefit of ever using a formula over a numerical solution to fit CPMG data that incorporates this? The applications in recent years from the Kay group for getting things like excited state structures, and the bench marks for the experiments themselves all require inclusion of all the physics. You cannot do this with formulas. You might find it interesting to read e.g. the comments on this thread: https://plus.google.com/s/cpmg%20glove It seems the future should instead go for stop the use of formulas and instead use numerically with accurate experimentally determined spin flip rates, R1s, carrier positions and chemical shifts. It's a serious point: people trying to get meaning from their data should really not use any of these formulas. As a first guess, fair enough. The parameters might not be wrong. But any user, especially one that doesn't know much about the details, stands a reasonable chance of getting a wrong answer. This can be avoided by insistence on doing things rigorously. You are very welcome to incorporate this formula. I have a version in C that is again much faster that you are welcome to get. I think it would help if you nudge them in a more numerical direction and force them to measure a full set of e.g. spin flip rates. There are a number of Kay papers you can cite that would very much support this. All best wishes, Andy _______________________________________________________ Reply to this item at: <http://gna.org/support/?3154> _______________________________________________ Message sent via/by Gna! http://gna.org/