Hi Ed, Please see the comments below...
Edward d'Auvergne wrote: > Hi, > > Sorry for the delayed response, the last few months for me have been > crazy. Please see below for more: > > > On Tue, Jun 2, 2009 at 8:36 PM, Sébastien > Morin<[email protected]> wrote: > >> Hi, >> >> This is a fairly old post, but I finally had time to think about these >> issues... Please see below... >> >> >> >> Edward d'Auvergne wrote: >> >>> Hi, >>> >>> Is the frequency for the reference spectrum necessary? Isn't >>> cmpg_delayT set to zero in this case, i.e. the CPMG block is missing? >>> If it is necessary though, a value of None is probably a better choice >>> to identify it rather than the frequency of zero Hz. >>> >> I guess recording a reference for each frequency is necessary since the >> intensity is to be extracted and could vary when changing magnet (along with >> S/N)... >> >> I agree for a value of None for the reference spectrum (which is what is >> presently in the code). >> > > Ok, so we need a reference frequency set, but cmpg_delayT set to None. > Fine. > >>> Another question I have is should the nu_cmpg value be given (with Hz >>> units), or would it be better if the omega_cmpg value was given (with >>> rad/s units)? If nu_cmpg is given, this will have to be converted >>> later to omega. I think we should have an explanation of both, after >>> the relevant model equations. Also the 'frq' arg of >>> relax_disp.cpmg_frq() might be better named as nu_cmpg or omega_cmpg >>> for clarity if this is frequency or angular frequency. >>> >> For this part, I am not sure about the units to use... 'cpmg_frq' needs to >> be of the same units as 'kex' and 'dw' (see equations below). I guess 'kex' >> and 'dw' should be in rad/s, so 'cpmg_frq' should also be in rad/s... >> >> Is it right ? >> >> Depending on the answer, 'cpmg_frq' will be renamed (to either 'cpmg_nu' or >> 'cpmg_omega'). >> > > I think we should use omega units (with the hidden radian unit). Do > you know what is normally used? > In the CPMGFit program by Art Palmer, the units seem to be seconds for both the tcp (with tcp = 1 / 4 cpmg_frq) and Tau (with Tau = 1 / kex) variables. Accordingly, if using the same approach, the units would be 1/s for both kex and cpmg_frq. Hence, I still hesitate. On one hand, the units should maybe be 1/s so the rates extracted with our approach are the same as obtained using CPMGFit. On the other hand, the units for kex and cpmg_frq should maybe be rad/s since they need to be the same as for dw (Hz), the chemical shift difference between the two states. I am still confused as you may see... > > >> -------------------------- >> >> FAST EXCHANGE >> >> / / kex \ 4 * cpmg_frq \ >> R2eff = R2 + Rex * | 1 - 2 * Tanh | ------------------ | * ------------- | >> \ \ 2 * 4 * cpmg_frq / kex / >> >> SLOW EXCHANGE >> / / dw \ 4 * cpmg_frq \ >> R2eff = R2A + kA - | Sin | -------------- | * ------------- | >> \ \ 4 * cpmg_frq / dw / >> >> where cpmg_frq = 1 / ( 4 * cpmg_tau ). >> >> >> >>> Also note that >>> we have to convert the cmpg_delayT value too. Unit analysis of the >>> equation >>> >>> R2eff = ( 1 / T ) * Ln( Icpmg / Iref ) >>> >>> shows this. R2 is in units of rad/s. T is input in seconds. 1/T is >>> frequency in nu units of Hz. Therefore we need to convert to the >>> radian units of angular frequency by multiplying by 2pi as 2pi/T is in >>> rad/s units. The natural logarithm of peak intensities is unitless >>> and dimensionless. >>> >> I just had a look at the reference dataset included in the test suite (from >> Hansen et al., J. Phys. Chem., 2008)... >> >> When treating the delay T as is (in seconds), I get the same values for >> R2eff as published in the paper (for the FF domain). However, if multiplying >> the delay T by 2pi, I get values for R2eff that a way too big. >> > > delay T is in the pulse sequence and should be in seconds. > Fine. > >> I do not want to say that the logic behind unit analysis is deficient. I >> agree with that logic, but I also think that, in this case, the delay T >> should stay in seconds in order to get R2eff values of the good size... >> > > Despite delay T being in seconds, R2eff is in rad/s. This is the same > as standard R1 or R2 where the time period in the pulse sequence is in > seconds whereas the fitted rate is in rad/s. > Fine. > >> What do you think ? >> > > As long as a number of published results can be replicated, we should be fine. > I agree. Regards, Séb > Regards, > > Edward > > -- Sébastien Morin PhD Student S. Gagné NMR Laboratory Université Laval & PROTEO Québec, Canada _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
