Hi Edward, I did what you said and deselected the spins showing a non-exponential behaviour and it worked! Thank you!
Cheers, Oliver -- Oliver Arnolds, M.Sc. AG Biomolekulare NMR (NC5/173) Faculty of Chemistry and Biochemistry Ruhr-University Bochum Universitaetsstrasse 150 44801 Bochum Germany Tel.: +49 234 32-26246 Am 18.06.19, 10:16 schrieb "Edward d'Auvergne" <[email protected]>: On Mon, 17 Jun 2019 at 15:36, Oliver Arnolds <[email protected]> wrote: > > Dear all, > > after some time now I installed the GUI version of relax4.1.2 on Ubuntu 18.04.2 LTS (with 16GB RAM and an i7 7700 CPU @3,6 GHz x8 processor) and repeated the R1 determination with the same result. After doing the grid search successfully the Monte Carlo simulations run for a few seconds until around simulation 20 and then get stuck there. Unfortunately I don't get an error message and I can still navigate between open relax windows so the program itself does not appear to have crashed. I tried this now on three different computers (2 Macs and 1 Ubuntu, everytime with the relax GUI) always getting the same result. As far as I can tell I did the setup as described in the manual but maybe I did a mistake there? > I use the sparky format for the peak lists from single-scan interleaved spectra and read out the heights of the signals. Regarding the spins I select the N and H spins for the backbone amides, for error analysis I use two triplicated spectra. > > Any ideas are highly appreciated, thanks in advance! Hi Oliver, Please plot your R1 and R2 curves. The reason MC simulations take a long time is only one thing - the fitting of an exponential to bad data X number of times can take a very long time, especially if the curve is flat or is not an exponential. Fitting exponentials is only fast if the data you fit is exponential, otherwise it can be incredibly slow. You really need to look at the quality of the input data. Try loading all the data into the relax GUI, but don't click on the execute button. Instead run the grace.write user function from the menus. For the X data type select "relax_times". For the Y data type select "peak_intensity". And set the file name to "intensities.agr" and click on the "Apply" button. Then change the file name to "intensities_norm.agr", set the normalisation flag to "True" and click on "OK". You'll then have 2 Grace plots for visualising the exponential curves [1]. Look at these very carefully and make sure that all curves really are exponentials. These plots are very useful for trimming the input data. You can then deselect the spins in the GUI prior to running the analysis. I hope this helps. Regards, Edward [1] https://en.wikipedia.org/wiki/Grace_(plotting_tool) _______________________________________________ nmr-relax-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/nmr-relax-users _______________________________________________ nmr-relax-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/nmr-relax-users
