While we are on the topic of model selection/optimization, I am having some trouble with relax 1.2's full_analysis.py script. I have optimized the local_tm run, and I ran the initial run on the oblate tensor (init). When I attempt to optimize the oblate run (round_1), I see the following error a:
relax> results.write(run='final', file='results', dir='oblate/round_1/ aic', force=1, format='columnar', compress_type=1)Opening the file 'oblate/round_1/aic/results.bz2' for writing.RelaxError: The sequence data for the run 'final' does not exist. Any ideas? Thanks, Doug On Apr 30, 2007, at 10:11 AM, Clare-Louise Evans wrote: > Dear Edward, > > Sorry for the thread hijack, but I noticed in the PS section of the > quote Hongyan has included below your comment regarding convergence. > > I am having problems with convergence at the moment when running the > full_analysis.py script. I have run the optimisation of the diffusion > models on the same PC. For the oblate, prolate and ellipsoid models I > have failed to reach convergence after 30+ rounds. The sphere model > converged within 5 rounds. However, when I look at the output the > only > difference between the chi-squared and other parameter values is in > the > 10th and later decimal places. Surely, with having such small > differences between the values they can be considered to have > converged. However, in your comment you state they have to be > identical. If this really is the case then I'm not sure how to > proceed > given that I'm failing to reach convergence on these 3 models? > > Apologies if this ties in to the question I asked yesterday regarding > full_analysis.py. > > Kind regards > Clare > > Hongyan Li wrote: >> Dear Edward, >> Thanks for your early suggestion regarding different model >> selections. I have >> been busy on other stuff and only recently got time to focus on >> this subject >> again. >> I have run all the diffusion models e.g. isotropic, prolate, >> oblate and >> ellipsoid and model selections were made within each model (in aic >> directory). >> I am not sure how to write a script to select different models using >> 'model_selection()'. Could you please do me a favor? >> Your help is highly appreciated! >> Best wishes, >> Hongyan >> >> Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: >> >> >>> Hi, >>> >>> To compare the results what you need to employ is a technique >>> from the >>> statistical field of model selection. The spherical diffusion >>> (isotropic) + all model-free models of all selected residues is one >>> single mathematical model. The prolate and oblate spheroids >>> (prolate >>> and oblate axially symmetric anisotropic diffusion tensors) + all >>> model-free models, and the ellipsoid (fully anisotropic or three >>> different eigenvalues) + all model-free models, are three additional >>> mathematical models. Therefore to compare these four different >>> models >>> you need to select the model which best represents your relaxation >>> data. These models are, however, not nested and therefore cannot be >>> compared using ANOVA F-tests! Firstly the three types of diffusion >>> tensor are not nested (there is a reference from Dominique Marion's >>> group in which they say ANOVA statistics cannot be used but I can't >>> find it at the moment (although it shouldn't be too hard to track >>> down, it's related to Tensor)). Secondly the model-free models >>> selected will be different between the four models. Hence chi- >>> squared >>> and F-tests cannot be used. >>> >>> A useful reference (I'm not at all biased ;) for this problem is my >>> paper d'Auvergne, E. J. and Gooley, P. R. (2003), (see >>> http://www.nmr-relax.com/refs.html for the full reference). On page >>> 37 at the end of that paper I discuss how AIC model selection is >>> perfect for selecting between these non-nested models. The AIC >>> criterion is still >>> >>> AIC = chi2 + 2k, >>> >>> however chi2 is the minimised chi-squared value for the complete >>> model >>> and k is the sum of the number of diffusion parameters and number of >>> model-free parameters for all spin systems. BIC model selection is >>> likely to work quite well as well. If you have four runs, one for >>> each of the diffusion models, then the relax user function >>> 'model_selection()' is designed to select between these models. I >>> hope this helps and hasn't been too biased. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> P.S. Prior to model selection between the diffusion models, the >>> diffusion models must have fully converged. Multiple iterations of >>> optimisation of the model-free models, AIC model selection, and >>> optimisation of all parameters together (diffusion tensor + model- >>> free >>> parameter of all residues) must be executed. Convergence is when >>> two >>> iterations possess identical chi-squared values, identical model- >>> free >>> models, and identical parameter values. >>> >>> >>> On 3/2/07, Hongyan Li <[EMAIL PROTECTED]> wrote: >>> >>>> Dear relax users, >>>> I have managed to use Relax to run my dynamics data by both >>>> isotropic and >>>> axial-oblate models. My qestion is how to compare the results, by >>>> >>> chi-square?? >>> >>>> what is the criteria to make judgment that which residues is beter >>>> >>> simulated >>> >>>> with which model? >>>> >>>> Thanks for your kind help! >>>> >>>> Best wishes, >>>> >>>> Hongyan >>>> >>>> Dr. Hongyan Li >>>> Department of Chemistry >>>> The University of Hong Kong >>>> Pokfulam Road >>>> Hong Kong >>>> >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-users mailing list >>>> [email protected] >>>> >>>> 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 >>>> >>>> >> >> >> Dr. Hongyan Li >> Department of Chemistry >> The University of Hong Kong >> Pokfulam Road >> Hong Kong >> >> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users mailing list >> [email protected] >> >> 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 >> > > This message has been checked for viruses but the contents of an > attachment > may still contain software viruses, which could damage your > computer system: > you are advised to perform your own checks. 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