Re: model selectionRe: model selectionDear 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 modelconverged within 5 rounds. However, when I look at the output the only difference between the chi-squared and other parameter values is in the10th 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 beidentical. If this really is the case then I'm not sure how to proceedgiven 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: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.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 subjectagain.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 <edward.dauvergne@xxxxxxxxx>:Hi,To compare the results what you need to employ is a technique from thestatistical field of model selection. The spherical diffusion (isotropic) + all model-free models of all selected residues is onesingle mathematical model. The prolate and oblate spheroids (prolateand 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 additionalmathematical models. Therefore to compare these four different modelsyou 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 modelsselected will be different between the four models. Hence chi- squaredand 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 modeland 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, andoptimisation 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- freemodels, and identical parameter values. On 3/2/07, Hongyan Li <hylichem@xxxxxxxxxxxx> wrote:Dear relax users,I have managed to use Relax to run my dynamics data by both isotropic andaxial-oblate models. My qestion is how to compare the results, bychi-square??what is the criteria to make judgment that which residues is betersimulatedwith 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 relax-users@xxxxxxx 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-usersDr. 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 relax-users@xxxxxxx 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 relax-users@xxxxxxx 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 relax-users@xxxxxxx 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.