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.


> Am 10.08.2016 um 16:37 schrieb Johannes Dietschreit <dietschr...@gmail.com>:
> 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 <dietschr...@gmail.com 
> <mailto:dietschr...@gmail.com>>:
> 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 xh_vector_dist.py, but I am not 
> sure whoch file should be the  input for
> 'select.read(file=pardir+sep+'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 <edw...@nmr-relax.com 
> <mailto:edw...@nmr-relax.com>>:
> 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 <dietschr...@gmail.com 
> <mailto:dietschr...@gmail.com>> 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. (http://dx.doi.org/10.1007/s10858-007-9214-2 
> <http://dx.doi.org/10.1007/s10858-007-9214-2>)
> 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:
> http://www.nmr-relax.com/api/4.0/auto_analyses.dauvergne_protocol-module.html 
> <http://www.nmr-relax.com/api/4.0/auto_analyses.dauvergne_protocol-module.html>
> http://www.nmr-relax.com/api/4.0/auto_analyses.dauvergne_protocol.dAuvergne_protocol-class.html
> <http://www.nmr-relax.com/api/4.0/auto_analyses.dauvergne_protocol.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 (
> http://www.nmr-relax.com/manual/Model_free_analysis_in_reverse.html 
> <http://www.nmr-relax.com/manual/Model_free_analysis_in_reverse.html> ),
> 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 dauvergne_protocol.py 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 ( http://gna.org/support/?func=additem&group=relax 
> <http://gna.org/support/?func=additem&group=relax> ).  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
> http://www.nmr-relax.com/manual/Temperature_control_and_calibration.html 
> <http://www.nmr-relax.com/manual/Temperature_control_and_calibration.html>
> , 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/xh_vector_dist.py 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.
> (http://dx.doi.org/10.1007/s10858-007-9213-3 
> <http://dx.doi.org/10.1007/s10858-007-9213-3>)
> 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: dietschr...@gmail.com

relax (http://www.nmr-relax.com)

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