Dear Christina.
I think Edward is on vacation, but maybe I can help.
I have only worked on the dispersion part of relax and by no means
expert on the model free part.
But I understand the data structure of relax and can maybe help with a
script for your analysis.
Can you provide a description of where you are in the process, and
what you aim for.?
Best Troels
Den 13. nov. 2015 12.12 PM skrev "Christina Möller"
<c.moeller@xxxxxxxxxxxxx <mailto:c.moeller@xxxxxxxxxxxxx>>:
Dear Edward,
thank you so much for your recommendations and the really helpful wiki
article about the CGS and SI unit system. Now I understand the
equation
differences and successfully back-calculated my relaxation data.
Furthermore, I used the generate_ri.py script and the back-calculated
values are close to the experimental data (as expected). I have to
admit
that I copied the motion parameters (s2,sf2,s2s,tf, etc) and the
associated model manually into the script and executed the script
several times for different residues. I am pretty sure that it is
possible to include one or several lists in order to automatically
update these parameters for each residue and run this script only one
time. Unfortunately, I was not able not find out how this works. Could
you give me an idea?
Thanks,
Christina
Am 11/05/2015 um 03:53 PM schrieb Edward d'Auvergne:
Hi Christina,
Please see below:
On 5 November 2015 at 14:05, Christina Möller
<c.moeller@xxxxxxxxxxxxx <mailto: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
--
------------------------------------------------------------
Christina Möller
ICS-6 / Structural Biochemistry
Forschungszentrum Jülich
D-52425 Jülich
GERMANY
E-mail: c.moeller@xxxxxxxxxxxxx <mailto:c.moeller@xxxxxxxxxxxxx>
Tel.: +49-2461-619387 <tel:%2B49-2461-619387>
Fax +49-2461-619387 <tel:%2B49-2461-619387>
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Re: back calculation of relaxation data