2009/8/25 Sébastien Morin <sebastien.morin.1@xxxxxxxxx>:
Hi Ed,
Please see the comments below...
Mine too :)
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<sebastien.morin.1@xxxxxxxxx> 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:
[snip]
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.
Is this really 1/s or Hz? If we use either 'cpmg_nu' or 'cpmg_omega'
rather than 'cpmg_frq' and specify the units, then the user should
never have issues working this out. From the equations you gave
previously, the sin() function gives a clue. I think the frequency is
Hz.
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.
I think we should have a system test set up which says that the result
must be that obtained by CPMGFit. This will then only pass when relax
is producing exactly the same result (which is what the aim should
be).
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...
I think that we just have to clearly state which is being input or
being output - i.e. unhide the hidden radian unit when present. And
this radian unit must balance (and also be only one radian unit in the
sin() function). If there are any variables we have problems
determining if the hidden unit is present, we could ask Art Palmer as
he is well aware of all these units.
Cheers,
Edward
Re: r8343 - in /branches/relax_disp: prompt/relax_disp.py specific_fns/relax_disp.py