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 <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) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
