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.
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. 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.
Regards,
Edward
On Thu, Jan 8, 2009 at 8:13 PM, <sebastien.morin.1@xxxxxxxxx> 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
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Re: r8343 - in /branches/relax_disp: prompt/relax_disp.py specific_fns/relax_disp.py