Douglas, Did the suggestion by Clare help fix the issue? Unless you have modified the script, full_analysis.py takes your amino acid sequence from the PDB file and hence the heteronuc='N', proton='H' arguments to the 'pdb()' user function may need to be changed for your structure. Otherwise if this is not the issue would you be able to create a bug report at https://gna.org/bugs/?func=additem&group=relax? Thanks. Any additional information would be much appreciated.
Thanks, Edward On 4/30/07, Douglas Kojetin <[EMAIL PROTECTED]> 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 > _______________________________________________ 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
