Hi,
This is not directly calculated as most models don't use omega_eff,
but rather the rotating frame tilt angle theta. But support for this
would be trivial. Just create a new module called lib.rotating_frame,
for example as this is independent of dispersion, and add a function
called something like calc_omega_eff(). It would take as arguments
the Lamor frequency of the spin (population averaged for exchange
processes), the spin-lock offset (or hard pulse offset), and the
spin-lock field strength (or pulse strength). Then just use the basic
formula (see table 10.2 of the relax manual) to calculate the value
per spin, experiment type, and magnetic field.
Alternatively you could modify the
specific_analyses.relax_disp.disp_data.return_offset_data() function
to calculate the value at the same time it calculates theta.
Regards,
Edward
On 5 March 2014 14:25, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
Dear Edward.
Would it be possible to implement the calculation of the parameter:
w_e ? The Omega_eff (Effective field in the rotating frame) ?
http://www.nmr-relax.com/manual/Dispersion_model_summary.html
As seen in the model DPL94 for 2-site off-resonance fast exchange
relaxation.
http://wiki.nmr-relax.com/DPL94
This would come in handsome for producing .out files with w_e and for
the wished plotting
feature.
Best
Troels
2014-02-28 10:33 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Either option would be reasonable. I would suggest, for design and
implementation simplicity, to choose the option to modify the current
relax_disp.plot_disp_curves user function. The 2D graphs, whether the
x-axis is the offset or dispersion point (spin-lock field or nu_CPMG
value) are all dispersion curves so it would also make more sense for
the user. You could also look at the grace.write user function for
inspiration. That user function is far more advanced in its options,
and you may have interest in replicating some of that functionality as
well.
Regards,
Edward
On 28 February 2014 09:54, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>
wrote:
Dear Edward.
I think I would let you decide where such a function resides best. :-)
I simply don't have the insight yet to make such decisions.
Best
Troels
2014-02-28 9:46 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi,
Note that this could be used for CPMG-type data as well, if a user
decides to change the hard pulse offset and run multiple experiments.
It's very unlikely to ever happen, but if added for R1rho, it could
just as easily be added for all data types.
Regards,
Edward
On 28 February 2014 09:43, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:
Hi,
I always wanted to add this, but never found the time. For an
implementation, what do you propose? Maybe the
relax_disp.plot_disp_curves user function could modified to allow the
X-axis to be specified. Or maybe a new user function based on
relax_disp.plot_disp_curves could be created.
Regards,
Edward
On 28 February 2014 09:39, Troels E. Linnet
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/support/?3124>
Summary: Grace graphs production for R1rho analysis
with
R2_eff as function of Omega_eff
Project: relax
Submitted by: tlinnet
Submitted on: Fri 28 Feb 2014 08:39:58 AM UTC
Category: None
Priority: 5 - Normal
Severity: 2 - Minor
Status: In Progress
Assigned to: tlinnet
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Operating System: None
_______________________________________________________
Details:
For an auto analysis of R1rho, relax produces graphs with
R1rho (Relaxation rate in the absence of exchange) [rad/s] as function
of
Omega_rf (Spin-lock offset, the frequency of the of RF field) [rad/s].
Such graphs can be quite crowded, since for a recorded dataset with for
example a variation of 6 spin-lock offset in ppm, the graphs will
contain 6
legends.
It is suggested to also provide graphs with R2_eff as function of
Omega_eff
(Effective field in the rotating frame) [rad/s].
An example of such a graph is figure 2 in
http://dx.doi.org/10.1021/bi4001062.
Both types of figures are attached.
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Fri 28 Feb 2014 08:39:58 AM UTC Name: disp_52_N.png Size: 13kB
By:
tlinnet
<http://gna.org/support/download.php?file_id=20207>
-------------------------------------------------------
Date: Fri 28 Feb 2014 08:39:58 AM UTC Name:
Figure2_Kjaergaard_et_al_2013_Off-resonance_R1rho_relaxation_dispersion_experiments_using_the_DPL_model.png
Size: 123kB By: tlinnet
<http://gna.org/support/download.php?file_id=20208>
_______________________________________________________
Reply to this item at:
<http://gna.org/support/?3124>
_______________________________________________
Message sent via/by Gna!
http://gna.org/
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-devel mailing list
relax-devel@xxxxxxx
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
Re: [sr #3124] Grace graphs production for R1rho analysis with R2_eff as function of Omega_eff