Dear Douglas, I kept getting this same error when I first tried using relax. after checking all the input formats, it turned out to be that it wasn't finding the NH vectors because of the H atoms in my pdb. I found simply changing the HN atoms to H rectified this. Whether this was the true reason I'm unsure, but the error message stopped after I did this.
Hope this helps. Clare Douglas Kojetin wrote: > 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. Email communications >> with the >> University of Nottingham may be monitored as permitted by UK >> legislation. >> >> >> _______________________________________________ >> 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 >> > > > _______________________________________________ > 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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