Hi,
For the definitions for the different dispersion models, you should
look at the code in the lib.dispersion modules. In each case it is
handled differently. Which value are you after exactly? If you are
after the measured exponential relaxation rate, directly from the NMR
spectrum, that would be spin.r2eff (either from the exponential curve
or the two point approach). If you are interested in the R2eff value
from the fitted parameters for the specific model, which is what those
equations look like, that would be the back-calculated value stored in
spin.r2eff_bc. If you are interested in the pure on-resonance R1rho'
value with no exchange, that would be spin.r20.
From the equations, it looks like you are after the on-resonance R1rho
value with exchange. Is this correct? This value is never calculated
or stored in relax as it serves no purpose. Are you really sure this
is what you are after, and not the back-calculated value which should
match the experimental values? If you are really sure, then I suppose
it could be calculated. But this would have to be done for all the
different R1rho dispersion models, and each is different. You would
have to call the functions of lib.dispersion (for every dispersion
model this will be different), and set the rotating frame tilt angle
to zero. Then the back_calc data structure will contain the required
values. I have a feeling that this is not what you are after though.
Regards,
Edward
On 12 March 2014 18:08, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
Hi Edward.
I am looking to calculate
R2_eff = spin.r20 + (phi_ex * k_ ex )/ (k_ex^2+w_e^2 )
R2_eff = (spin.r2eff - spin.ri_data['R1'] *cos(t)**2) / sin(t) **2
As also noted here
http://thread.gmane.org/gmane.science.nmr.relax.devel/5164
Best
Troels
Troels Emtekær Linnet
2014-03-12 17:45 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi Troels,
The R2_eff value stored in spin.r2eff should already contain the R1
contribution. Have a look lib.dispersion.dpl94. The spin.r2eff value
is equivalent to the back_calc value. If you would like to isolate
the pure R1rho contribution, that would be the spin.r20 parameter. So
maybe if you use grace.write with the theta parameter on the X-axis
and r20 on the Y-axis, this will already automatically work.
Regards,
Edward
On 12 March 2014 14:32, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
The two issues I am trying to resolve, is to make graphs of:
R2_eff as function of Omega_eff.
https://gna.org/support/?3124
where
R2,eff = (R1rho - R1*cos(t)*2) / sin(t) *2
I would implement another function to calculate this, as:
R1rho : spin.r2eff
R1 is the loaded R1 values : spin.ri_data
and theta I just calculated.
And plot R1rho as function of theta (and looping over offset).
I think I will now try to implement the relax_disp.write_disp_curves
for R1rho as function of theta.
best
Troels
Troels Emtekær Linnet
2014-03-12 13:54 GMT+01:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
Hi,
What does the output look like? Could you copy and paste an example?
I'm guessing the relax code is now fully functional so that these
files can be created. If so, then creating these files in the
auto-analysis would not be a problem. What is the plan for the
relax_disp.write_disp_curves user function?
Regards,
Edward
On 12 March 2014 13:43, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
Hi Edward.
I would like to add the custom to write out:
value.write(param='theta', file='theta.out')
value.write(param='w_eff', file='w_eff.out')
For those models who are in the list
MODEL_LIST_R1RHO_FULL = [MODEL_R2EFF, MODEL_NOREX, MODEL_M61,
MODEL_M61B,
MODEL_DPL94, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_R1RHO_2SITE,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]
"""The list of the R2eff model together with all dispersion models
specifically for R1rho-type experiments."""
In the relax_disp auto-analysis, in write_results()
I was thinking to add:
# The theta/w_eff parameter.
if model in MODEL_LIST_R1RHO_FULL:
self.interpreter.value.write(param='theta',
file='theta.out',
dir=path, force=True)
self.interpreter.value.write(param='w_eff',
file='w_eff.out',
dir=path, force=True)
Do you support this?
Best
Troels
Troels Emtekær Linnet
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Re: Adding value.write of theta/w_eff to auto-analysis of relax_didp for R1rho experiments.