Hi Chung-ke. Can you put the information about which version of relax you use?
You can in terminal do: relax -i and write it here. And then there is the question if you used data from one field or two spectrometer fields. Fitting to one field, can give problems. This is described here: """Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements.""" Kovrigin, Evgenii L; Kempf, James G; Grey, Michael J; Loria, J Patrick Journal of magnetic resonance, 2006, Vol 180, p 93-104. http://www.ncbi.nlm.nih.gov/pubmed/16458551 DOI: 10.1016/j.jmr.2006.01.010 Figure 9 and 10 shows these "rotten bananas". Clustering data, in some way overcome this problem. Since you now starts to add more data, compared to number of fitting parameters. The problem though, is that if you start from "single fitted" data, and go to "Clustering of data", that an average of the global parameter will be taken for the single fitted data. In previous version of relax (a version or two ago), we changed from taking the average to take the median of the parameters. This was to prevent taking the average of an outliers, if one of the single fitted spins have been fitted "crazy". You don't want to start with a global kex at 10000. I have discussed the CR72 Full model with my supervisor. He have actually never seen it in use in any paper. Always the assumption R20A=R20B is used. If you only have one field, I would not even try this model. If you still would like to try it, please consider using the B14 full model as well, to compare. http://wiki.nmr-relax.com/B14_full Abstract: "Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements." This work examines the robustness of fitting of parameters describing conformational exchange (k(ex), p(a/b), and Deltaomega) processes from CPMG relaxation dispersion data. We have analyzed the equations describing conformational exchange processes for the intrinsic inter-dependence of their parameters that leads to the existence of multiple equivalent solutions, which equally satisfy the experimental data. We have used Monte-Carlo simulations and fitting to the synthetic data sets as well as the direct 3-D mapping of the parameter space of k(ex), p(a/b), and Deltaomega to quantitatively assess the degree of the parameter inter-dependence. The demonstrated high correlation between parameters can preclude accurate dynamics parameter estimation from NMR spin-relaxation data obtained at a single static magnetic field. The strong parameter inter-dependence can readily be overcome through acquisition of spin-relaxation data at more than one static magnetic field thereby allowing accurate assessment of conformational exchange properties. Troels Emtekær Linnet PhD student Copenhagen University SBiNLab, 3-0-41 2014-09-09 9:48 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: > Hi Chung-ke, > > Welcome to the relax mailing lists! Thanks to the hard work of one of > the relax developers - Troels Linnet - this long calculation time > should now be much, much shorter. Have a look at the following > release announcement: > > http://wiki.nmr-relax.com/Relax_3.3.0 > > For the 'CR72 full' model (http://wiki.nmr-relax.com/CR72_full), the > clustering example here gives a ~22x speed up so your calculation time > would then drop from ~20,000 min to ~1000 min. If you would like to > receive announcements about new relax versions, please subscribe to > the relax-announce mailing list > (https://mail.gna.org/listinfo/relax-announce/). This list only > receives ~10 emails per year. See > http://news.gmane.org/gmane.science.nmr.relax.announce. > > I have a few questions about how you performed the analysis. Did you > use a non-clustered set of results to seed the clustered analysis? In > the dispersion auto-analysis protocol exposed via the GUI, the results > from the non-clustered analysis will be taken as the starting point > for optimisation of the clustered analysis, as described in Morin et > al., 2014 (http://dx.doi.org/10.1093/bioinformatics/btu166). If you > wish, and are capable with scripting, you can also create your own > analysis protocol via a relax script and not use the auto-analysis. > The relax software is very flexible and you can create quite complex > analysis protocols - the auto-analyses are just large relax scripts. > > Also, did you look at the results from the non-clustered analysis to > see if the kinetics of all 13 residues are similar? Or if the > dispersion curves look reasonable? Some data might be of low quality > and causing difficulties with the optimisation. You should also note > that most dispersion data is not good enough to differentiate R20A > from R20B. Do the final results (non-clustered and clustered) look > reasonable for these two parameters? It could be that differentiating > R20A from R20B in your system is difficult and causing optimisation to > take much longer than normal. Do you see the same optimisation times > with the clustered CR72 model where R20A=R20B=R20 > (http://wiki.nmr-relax.com/CR72)? Also, have a look at the log file > from the analysis and see if the total number of minimisation > iterations is much longer for the 'CR72 full' model compared to the > CR72 model. This will tell you if the optimisation problem is much > more complicated for the 'full' model. > > Regards, > > Edward > > > On 9 September 2014 09:19, Chung-ke Chang <chun...@ibms.sinica.edu.tw> wrote: >> Dear all, >> >> This is my first post here, and I have a question regarding the time it >> takes for a relaxation dispersion clustering process to finish. I have one >> clustering calculation that has been running for ~ 20,000 min on a single >> Xeon 2.66 GHz core. The cluster consists of 13 residues being fit to the >> ‘CR72 full’ model. I wonder if the long time it is taking is normal? Would >> it be possible that relax has been stuck in an infinite loop of some sort, >> without showing up in the log file? Any input would be greatly appreciated. >> By the way, using a cluster of only 11 residues out of the 13 did finish in >> ~13,000 min. >> >> Chung-ke Chang >> Biomacromolecular NMR Lab >> Institute of Biomedical Science >> Academia Sinica, Taiwan >> _______________________________________________ >> 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 > > _______________________________________________ > 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 _______________________________________________ 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
