Dear Johannes.

As far as I know, Edward is currently on maternity leave.

To solve this problem, it would be easier to have access to some of your
Can you upload to:

Take each of your data files, and delete all data, except 2 spins.
Also provide your script file, or a description of which button you press
in the GUI.

Please also provide information about your system with:
relax -i

Then I will make a tutorial for you. To be added here:

I have just made a similar tutorial here:

If there is a problem in relax, I will write a systemtest which will solve
the problem.
And the problem will never return.

If this a user error, the tutorial should help to prevent this, and would
be the first step before
adding/modifying the manual.

I can only help with setting up the loading of the data.
The interpretation of the results is not my strong side.


2016-08-24 17:27 GMT+02:00 Johannes Dietschreit <>:

> Hey guys,
> I just wondered whether you could help me finding the problem in my usage
> of relax or whether there is a problem with the data. Do you have any
> suggestions to the questions I have asked in the previous mails?
> Thank you in advance.
> Johannes
> Am 10.08.2016 um 16:37 schrieb Johannes Dietschreit <
> >:
> Hi,
> I wanted to ask whether there is an example data set of relaxation data,
> PDB and results that I could use to see whether I get the same results and
> thus am using the software correctly in order to find out whether it's the
> handling of the programm or the supplied data that causes trouble.
> Thanks for all your help!
> Johannes
> 2016-08-09 11:15 GMT+02:00 Johannes Dietschreit <>:
>> Hello Edward,
>> I understand that the strict convergence criteria are neccessary. When I
>> set the max_iter parameter to just 30, I get very similar results as to
>> when I reduce the opt_tol. I guess the model is just not converged.
>> You were quite right, the negative te values are very close to zero,
>> their error is many orders of magnitude larger than their own value. The
>> avergae hetNOE values is around 0.7. The measurements were taken at 600 and
>> 700 MHz. I haven't taken them myself, my work concerns the theoretical side
>> of things. The protein is not a membrane protein, it is in solution and the
>> exact molecule given in the crystal structure I used as input for relax was
>> measured (no tag or similar). The local spectrometer does unfortunately not
>> allow for fancy temperature control methods.
>> I feel relatively certain that the set up was in general correct. I tried
>> both your python script and the GUI. The results I reported were taken from
>> the txt-files in the final folder. As for the results of the previous runs.
>> I am not sure how to access them or to read them. They are all zipped xml
>> files where I cannot find a clear results section. Is there a certain
>> program/command I should use?
>> I wanted to use your visualization script, but I am not
>> sure whoch file should be the  input for
>> ''rates.txt', change_all=True,
>> res_num_col=2)'
>> I visualized the tensor.pdb which is printed in the final directory. It
>> is huge compared to the protein. It has the shape of a eight of a spheroid.
>> Maybe just a simple question regarding the input. The R1 and R2 input
>> files contained values in Hz (not radian). Is that correct?
>> Regards,
>> Johannes
>> 2016-08-08 16:49 GMT+02:00 Edward d'Auvergne <>:
>>> Hi Johannes,
>>> Sorry for the late response.  I've been quite busy in the last two
>>> months.  Please see below:
>>> On 8 August 2016 at 13:25, Johannes Dietschreit <>
>>> wrote:
>>> > Hi,
>>> >
>>> > thank you so much for your quick and long response. I did not change
>>> the
>>> > hard coded value, I decided to leave that one alone, but I followed the
>>> > example of the test_suite and set the convergence criterion to 1e-7.
>>> This
>>> > seems still strict, but now the calculation converges and final
>>> results are
>>> > written.
>>> The "strict" values are quite important for making sure there are no
>>> strange results.  You'll see that in:
>>>     d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
>>> dynamic models I. Minimisation algorithms and their performance within
>>> the model-free and Brownian rotational diffusion spaces. J. Biomol.
>>> NMR, 40(2), 107-119. (
>>> Reading this paper is essential for understanding these cut-off
>>> values, and why these high precision values are important.  However if
>>> there is a problem with the input data, then you will see problems.
>>> In your example, I am not sure why this is not stopping after 30
>>> iterations.  If you have a look at the automated protocol:
>>> tocol-module.html
>>> tocol.dAuvergne_protocol-class.html
>>> you will see the max_iter parameter.  Ok, I see that this is set to 30
>>> in the GUI, but it is not set in the sample script.  If you require
>>> more than 30 iterations of the global protocol (
>>> ),
>>> then this is an indication that the input data is problematic.
>>> > My question now regards the results in the folder "final". My analysis
>>> was
>>> > performed regarding the classical model free ansatz but I allowed for
>>> all
>>> > possible diffusion models. The protein I am dealing with is rather
>>> stiff,
>>> > it contains a beta barrel and some flexible loops. However, all
>>> residues
>>> > have a S^2 value of about 0.03. I expected the residues in the barrel
>>> to
>>> > have much larger values.
>>> These values indicate a severe problem with the input data.  What is
>>> your average HetNOE value?  At which field strengths did you measure?
>>> > Also the t_e values are somewhat spurious. Most of them are
>>> unphisically
>>> > small (~e-24 seconds), I had expected values in the range of ten to
>>> hundred
>>> > pico seconds. And there are a few t_e values with a negative sign. How
>>> is
>>> > that possible?
>>> These should disappear through model selection.  If te ~ 0, then the
>>> simpler model without te will be selected, as these models should have
>>> converged to the same result.  Unless of course there is a major
>>> failure of the whole analysis.  For the te values with negative
>>> values, what are there values?  The lower quality cut-off values will
>>> allow for very small minus te values.
>>> > Is this a common error? Have I just made a mistake regarding the
>>> input? I
>>> > attached my file and some input data.
>>> Note that you cannot attach files when posting to a public mailing
>>> list.  This is to avoid major strain on the infrastructure.  For
>>> sharing files, please create a support request and attach the files
>>> there ( ).  Be
>>> careful though, as this is public and anyone will be able to access
>>> your data.  From the ridiculously large number of iterations of the
>>> global algorithm and the non-physical S2 and te values, I can only
>>> guess that there is a major problem with the input data.  This could
>>> either be due to how the analysis was set up, or how the data was
>>> measured.  Looking at
>>> , how did you perform temperature calibration and temperature control?
>>>  Do you see any warnings at the start of your log files?  When running
>>> relax, it is extremely important to check every warning at the start
>>> to make sure that the results are reasonable.
>>> Also, if you look at the local tm model results, are the S2 and te
>>> values similar to the final results?  Or similar to the spherical
>>> diffusion model?
>>> Also note that for a rigid beta barrel with flexible loops that the
>>> backbone NH bond vector distribution will not be isotropic.  I suggest
>>> running the sample_scripts/ script and visualising
>>> the results.  This is the script I created for Figure 4 in:
>>>     d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
>>> dynamic models II. A new methodology for the dual optimisation of the
>>> model-free parameters and the Brownian rotational diffusion tensor. J.
>>> Biomol. NMR, 40(2), 121-133.
>>> (
>>> Also, are you in a membrane system?  If so, then you actually have two
>>> diffusion tensors.  The protein will spin inside the micelle/bicelle,
>>> and then the whole system will have an independent global ellipsoidal
>>> or spheroidal diffusion.  I am unaware of anyone to date who has
>>> derived the equations for such a system.  Nevertheless, the strange
>>> results you see are unlikely to be due to this modelling deficiency.
>>> Regards,
>>> Edward
> _______________________
> Johannes C. B. Dietschreit
> Leydenallee 83
> 12167 Berlin
> mobile: +49 171 53 54 78 1
> mail:
relax (

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