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. >> 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? > -------------------------- > > 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. > 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. > What do you think ? As long as a number of published results can be replicated, we should be fine. Regards, Edward _______________________________________________ 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
