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 data. Can you upload to: https://gna.org/bugs/?group=relax 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: http://wiki.nmr-relax.com/Category:Tutorials I have just made a similar tutorial here: http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi 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. Note: I can only help with setting up the loading of the data. The interpretation of the results is not my strong side. Best Troels 2016-08-24 17:27 GMT+02:00 Johannes Dietschreit <dietschr...@gmail.com>: > 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>: > >> 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>: >> >>> 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> >>> 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) >>> >>> 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_pro >>> tocol-module.html >>> http://www.nmr-relax.com/api/4.0/auto_analyses.dauvergne_pro >>> 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 ( >>> 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 ). 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 >>> , 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) >>> >>> 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
