Cheers, I won't try to find if there are problems with the Gna! (https://gna.org/) mail server then!
Regards, Edward On 25 February 2010 08:01, Carl Diehl <[email protected]> wrote: > Hi. > Well, the mail server said that it tried sending three times before giving > up. I believe it has something to do with the mail servers at the university. > > Anyway, sofar I've used relax 1.2.XX both for fitting and modelfree-selection. > Is there a any major difference in the fitting routines between the 1.2 and > the 1.3 line? > > So far I've used a modified full_analysis.py script (in relax 1.2.14) for > analysis which works well and is able to accurately reproduce older > modelfree-fits. I haven't made the transition into 1.3.4, since I would have > to change from runs into pipes. > > My basic idea is to rerun the my analysis script, only this time using the > Palmer model-selection instead of AIC, which I've been using sofar. > From an old fit using Modelfree4 and Fast-MF (1field only), I know that there > are only small differences in S2 compared to the 2field-data fitted using > relax. > I can easily redo my 2field fits using Modelfree4 and Fast-MF, although I > would prefer to use relax. Time-wise, the full_analysis scripts seems to be > much faster than the Fast-MF way. > > I'll take a look at the repository and try to see if I can get it to work. > > Regards, > Carl Diehl > _______________________________________ > Från: [email protected] [[email protected]] för Edward > d'Auvergne [[email protected]] > Skickat: den 24 februari 2010 16:07 > Till: Carl Diehl > Kopia: [email protected] > Ämne: Re: Palmer model selection > > Hi, > > It's strange that your mail bounced. Did you use a different email > address? Maybe the mail server was down for a little while :S As for > your question, did you use the Newton optimisation provided by relax > (via minfx https://gna.org/projects/minfx/) or did you use relax to > control Art Palmer's Modelfree4 program? If you have data at more > than one field strength, I would highly recommend you run relax-1.3.4 > (or the repository 1.3 version) with the full_analysis.py script and > then compare. This implements the new protocol I presented in: > > d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of the > model-free problem and the diffusion seeded model-free paradigm. Mol. > Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f) > > and: > > d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR > dynamic models II. A new methodology for the dual optimisation of the > model-free parameters and the Brownian rotational diffusion tensor. J. > Biomol. NMR, 40(2), 121-133. > (http://dx.doi.org/10.1007/s10858-007-9213-3) > > The advances implemented in this script solve many, if not all, of the > problems people encounter in a model-free analysis. And I would be > willing to bet that your results will be at least slightly different > and better after running this! > > As for re-implementing the Mandel et al., 1995 model selection in > relax, this depends on if you used relax or Modelfree4 as the > optimisation engine. In any case, what you can do is develop code > inside your own script to do this. If it works, then the code can be > tidied up and shifted into the core of relax for the benefit of all > other users (or it can be added as a sample script with your name at > the top, and maybe a in the end reference to help with citation > counts). The Mandel et al., 1995 paper would be the best reference to > start to implement this. And Wikipedia would also help. If you would > like to add code directly to relax to do this, that would be very much > accepted too. > > A good starting point would be my old code for implementing this model > selection. I've looked back at the history and found the file needed. > It is located in version 0.2 of relax (relax was called mf back > then): > > http://svn.gna.org/viewcvs/relax/ > > This line was last touched 7 years ago!!! Since then the file has > been deleted as it no longer was functional. Luckily having relax in > a repository means that any file from any point of time can be > accessed. Therefore it can be restored and added back to > generic_fns/model_selection.py. To make it functional again will > require a lot of work (see my previous message at > https://mail.gna.org/public/relax-users/2010-02/msg00003.html). But > the file is located at: > > http://svn.gna.org/viewcvs/relax/0.2/model_selection/palmer.py?rev=298&view=markup > > Actually, I found that the file was deleted at revision r697 in the > 0.3 line. The most up to date version before deletion is therefore: > > http://svn.gna.org/viewcvs/relax/0.3/model_selection/palmer.py?rev=696&view=markup > > I hope this helps! > > Cheers, > > Edward > > > > > On 24 February 2010 12:48, Carl Diehl <[email protected]> wrote: >> Hi. >> >> I got a bounce from the gna-server, so I'm sending this again. >> >> At the moment I have a bunch of data sets that have been fitted with >> relax-1.2.14 using the AIC model selection. >> My supervisor wants to test the data sets using the Palmer methodology >> instead of using AIC or something similar. >> >> I've used FAST Modelfree before, so for fast results I'm running that at the >> moment. >> Since I'm much more used to relax, I'd prefer to use that instead. >> >> In order to add the Chi2 and F-tests, is it possible to do this within a >> relax script or would I need to dig into the source code? >> >> /Carl >> >> >> ________________________________________ >> Från: Edward d'Auvergne [[email protected]] >> Skickat: den 12 februari 2010 11:34 >> Till: Carl Diehl >> Kopia: [email protected] >> Ämne: Re: Palmer model selection >> >> Hi, >> >> This model selection method used to be supported in relax. No one has >> used it in many, many years, so this code has deteriorated and appears >> not to work anymore. I think this was last used in the 0.3 relax >> versions well over 7 years ago. The deterioration might be related to >> relax now using proper STAR format parsing of Art's mfout file. The >> F-tests are only implemented in Modelfree4 and not relax, so this >> binary needs to be used as an optimisation engine in relax. >> >> At the moment I don't have the time to repair this. This requires >> minimally the extraction of the chi-squared values and F-test info >> from the modelfree4 mfout file. This code is so old though that it >> may require adding the functionality to execute Modelfree4 with the >> model pairs to produce the F-test info. Alternatively if relax is >> used as the optimisation engine, the chi-squared and F-tests could be >> added directly to relax. In any case, this won't be trivial. But if >> anyone would like to contribute this functionality, it would be most >> welcome for comparisons and historical purposes. If you require fast >> results, I would recommend looking at the FAST ModelFree >> (http://xbeams.chem.yale.edu/~loria/software.php) or Art's scripts. >> >> Regards, >> >> Edward >> >> >> >> On 12 February 2010 10:50, Carl Diehl <[email protected]> wrote: >>> Hi. >>> Is there any version of relax with a working model selection using the >>> Palmer method? >>> Both in relax-1.2.15 and -1.3.4 the method don't seem to be supported? >>> >>> If not, how difficult would it be to implement it in relax? >>> >>> Regards, >>> Carl Diehl >>> Biophysical Chemistry >>> Lund University >>> _______________________________________________ >>> 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
