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).
>
> 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').
--------------------------
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.
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...
What do you think ?
Regards,
Séb :)
>
> Regards,
>
> Edward
>
>
> On Thu, Jan 8, 2009 at 8:13 PM, <[email protected]> wrote:
>> Author: semor
>> Date: Thu Jan 8 20:13:00 2009
>> New Revision: 8343
>>
>> URL: http://svn.gna.org/viewcvs/relax?rev=8343&view=rev
>> Log:
>> Added the user function cpmg_frq() and added examples to the user function
>> cpmg_delayT().
>>
>>
>> Modified:
>> branches/relax_disp/prompt/relax_disp.py
>> branches/relax_disp/specific_fns/relax_disp.py
>>
>> Modified: branches/relax_disp/prompt/relax_disp.py
>> URL:
>> http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/relax_disp.py?rev=8343&r1=8342&r2=8343&view=diff
>> ==============================================================================
>> --- branches/relax_disp/prompt/relax_disp.py (original)
>> +++ branches/relax_disp/prompt/relax_disp.py Thu Jan 8 20:13:00 2009
>> @@ -62,6 +62,15 @@
>> ~~~~~~~~~~~
>>
>> This user function allows the CPMG constant time delay (T) of a
>> given experiment to be set.
>> +
>> +
>> + Examples
>> + ~~~~~~~~
>> +
>> + To set a CPMG constant time delay T of 20 ms (0.020 s) for
>> experiments '600', type:
>> +
>> + relax> relax_disp.cpmg_delayT('600', 0.020)
>> + relax> relax_disp.cpmg_delayT(id='600', delayT=0.020)
>> """
>>
>> # Function intro text.
>> @@ -83,6 +92,39 @@
>> relax_disp_obj.cpmg_delayT(id=id, delayT=delayT)
>>
>>
>> + def cpmg_frq(self, frq=0, spectrum_id=None):
>> + """Set the CPMG frequency associated with a given spectrum.
>> +
>> + Keyword arguments.
>> + ~~~~~~~~~~~~~~~~~~
>> +
>> + frq: The frequency, in Hz, of the CPMG pulse train.
>> +
>> + spectrum_id: The spectrum identification string.
>> +
>> +
>> + Description
>> + ~~~~~~~~~~~
>> +
>> + This user function allows the CPMG pulse train frequency of a given
>> spectrum to be set.
>> + If a value of 0 is set for frequency, then the spectrum will be
>> treated as a reference
>> + spectrum.
>> +
>> +
>> + Examples
>> + ~~~~~~~~
>> +
>> + To identify the reference spectrum called 'reference_spectrum',
>> type:
>> +
>> + relax> relax_disp.cpmg_frq(0, 'reference_spectrum')
>> + relax> relax_disp.cpmg_frq(frq=0, spectrum_id='reference_spectrum')
>> +
>> + To set a frequency of 200 Hz for the spectrum '200_Hz_spectrum',
>> type:
>> +
>> + relax> relax_disp.cpmg_frq(200, '200_Hz_spectrum')
>> + relax> relax_disp.cpmg_frq(frq=200, spectrum_id='200_Hz_spectrum')
>> +
>> +
>> def exp_type(self, exp='cpmg'):
>> """Function for the selection of the relaxation dispersion
>> experiments to analyse.
>>
>>
>> Modified: branches/relax_disp/specific_fns/relax_disp.py
>> URL:
>> http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_disp.py?rev=8343&r1=8342&r2=8343&view=diff
>> ==============================================================================
>> --- branches/relax_disp/specific_fns/relax_disp.py (original)
>> +++ branches/relax_disp/specific_fns/relax_disp.py Thu Jan 8 20:13:00 2009
>> @@ -173,7 +173,7 @@
>> def cpmg_frq(self, frq=0, spectrum_id=None):
>> """Set the CPMG frequency associated with a given spectrum.
>>
>> - @keyword frq: The frequency, in Hz, of the CPMG train.
>> + @keyword frq: The frequency, in Hz, of the CPMG pulse
>> train.
>> @type frq: int
>> @keyword spectrum_id: The spectrum identification string.
>> @type spectrum_id: str
>>
>>
>> _______________________________________________
>> relax (http://nmr-relax.com)
>>
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>
> _______________________________________________
> relax (http://nmr-relax.com)
>
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--
Sébastien Morin
PhD Student
S. Gagné NMR Laboratory
Université Laval & PROTEO
Québec, Canada
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