Hi Christina,
Please see below:
On 5 November 2015 at 14:05, Christina Möller <c.moeller@xxxxxxxxxxxxx> wrote:
Dear Edward and relax-users,
I am sorry to ask you again for some advice to back calculate the relaxation
data from the model parameter values. Here is what I tried so far:
For the back calculation I loaded the final results determined by the
automated analysis using the dauvergne_protocol.py into the relax gui. Then
I selected the back_calc tool from user functions -> relax_data.
After starting the back calculation without any entry
relax> relax_data.back_calc(ri_id=None, ri_type=None, frq=None)
I get the following error message:
RelaxWarning: comparison to `None` will result in an elementwise object
comparison in the future.
This is a warning produced by more recent versions of the numpy Python
package. It is harmless message about changes which will occur in
numpy, and it is safe to ignore. Note that I have fixed this in the
source code repository and the fix will appear in the future when I
release relax 4.0.1 (it is not present in relax 4.0.0 at
http://wiki.nmr-relax.com/Relax_4.0.0 ). This was first reported at:
[relax-users] RelaxWarning: comparison to `None` will result in an
elementwise object comparison in the future (
http://thread.gmane.org/gmane.science.nmr.relax.user/1839 ).
And the solution at:
[relax-users] Re: RelaxWarning: comparison to `None` will result
in an elementwise object comparison in the future (
http://thread.gmane.org/gmane.science.nmr.relax.user/1844 ).
If I put the frequency in
relax> relax_data.back_calc(ri_id=None, ri_type=None, frq=599468076.0)
I get another error message
Traceback (most recent call last):
File
"/opt/scisoft64/usr/lib/python2.7/site-packages/relax/gui/interpreter.py",
line 306, in run
fn(*args, **kwds)
File
"/opt/scisoft64/usr/lib/python2.7/site-packages/relax/pipe_control/relax_data.py",
line 132, in back_calc
spin.ri_data_bc[ri_id] = api.back_calc_ri(spin_index=spin_index,
ri_id=ri_id, ri_type=ri_types[ri_id], frq=frqs[ri_id])
KeyError: 'R1_600'
Can you give me a hint what I am doing wrong?
I would suggest using the sample_scripts/model_free/generate_ri.py
sample script. The relax_data.back_calc user function requires that
the relaxation data ID, the relaxation type, and frequency arguments
be supplied to correctly calculate the desired data (see
http://www.nmr-relax.com/manual/relax_data_back_calc.html ). Without
this information, relax cannot determine what you would like to do.
Using the sample script would be the easiest option.
I know that the relaxation data can also be back calculated using the
equations 7.3a - 7.8 in the relax manual (PDF), although it is not that
trivial for an ellipsoid model because I need to determine the weights. Is
there a reason why you define c=1/3(ωH*∆σ)^2 (eq. 7.5) instead of
c=2/15(ωN*∆σ)^2 like it can be found in literature?
These two factors come from using CGS vs. SI units. I have mentioned
this issue before (see
http://thread.gmane.org/gmane.science.nmr.relax.devel/1023/focus=1034
). I have also started a stub wiki article to help explain these
differences - http://wiki.nmr-relax.com/CGS_versus_SI . In SI units
the correct unit (squared) is (ω·∆σ)^2 / 3, and SI units are used
throughout relax. This has made some parts of relax more difficult to
implement as there are many equations in the literature in CGS units,
and the authors will often not identify this older system. Some
stubborn people just prefer the magnetic constant to be 1 rather than
µ0/(4π), and will not shift from the CGS metric system to the SI
metric system.
Regards,
Edward
Re: back calculation of relaxation data