Hi Ed, Basic question,
relax only consider the relaxation data from one field to calculate the reduced spectra density mapping at three frequencies. Shouldn't one use at least three independent data sets (three fields) to calculate these three parameters. Best Regards Daniel [EMAIL PROTECTED] wrote: > Send relax-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.gna.org/listinfo/relax-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of relax-users digest..." > > > Today's Topics: > > 1. Re: Reduced spectral density mapping (Edward d'Auvergne) > 2. Re: Convergence on different systems (Edward d'Auvergne) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 3 Dec 2006 01:50:45 +1100 > From: "Edward d'Auvergne" <[EMAIL PROTECTED]> > Subject: Re: Reduced spectral density mapping > To: "Sebastien Morin" <[EMAIL PROTECTED]> > Cc: [email protected] > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=WINDOWS-1252; format=flowed > > Hi, > > Reduced spectral density mapping is a direct calculation of the > spectral density values, there is no optimisation. The only part > where optimisation could be used, but is not necessary, is in the > calculation of the single J(0) value using data at multiple field > strengths. See Kroenke et al., 1999 for details (Kroenke, C. D., > Rance, M. and Palmer, A. G. (1999). Variability of the 15N chemical > shift anisotropy in Escherichia coli ribonuclease H in solution. J. > Am. Chem. Soc. 121, 10119-10125). relax can't do this yet though > (although anyone is free to add that feature). > > Edward > > > On 12/2/06, Sebastien Morin <[EMAIL PROTECTED]> wrote: > >> Hi Edward >> >> Thanks for your help. >> >> I have another question about reduced spectral density mapping. >> >> With the script jw_mapping.py, one has to select the frequency >> (jw_mapping.set_frq()). I would like to know if it is possible to select >> datasets at multiple fields and then optimize everything together... >> Would this lead to better values as is the case with the model-free >> approach ? >> >> I tried by simply putting three fields : >> >> =============================================================== >> jw_mapping.set_frq(name, frq=499.719 * 1e6, frq=599.739 * 1e6, >> frq=799.744 * 1e6) >> =============================================================== >> >> but as I thought, ended up with an error : >> >> =============================================================== >> SyntaxError: duplicate keyword argument >> =============================================================== >> >> Of course... >> >> Thanks for help ! >> >> >> Séb :) >> > > > > ------------------------------ > > Message: 2 > Date: Sun, 3 Dec 2006 02:02:53 +1100 > From: "Edward d'Auvergne" <[EMAIL PROTECTED]> > Subject: Re: Convergence on different systems > To: "Sebastien Morin" <[EMAIL PROTECTED]> > Cc: [email protected] > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Convergence when using Newton optimisation in relax (or in any > application) should be quite fast. The Newton algorithm has what is > known as quadratic convergence - the fastest type of convergence. In > comparison steepest descent has linear convergence and the BFGS > algorithm has super-linear convergence. For more details see, for > example, Nocedal, J. and S. J. Wright: 1999, Numerical Optimization, > Springer Series in Operations Research, New York: Springer-Verlag. > Because of the quadratic convergence, tiny parameter differences will > most likely never occur and hence the convergence tests for identical > values won't be an issue. These tests for identical values will not > increase the amount of CPU time required relative to approximate value > tests where a small tolerance is added. > > The only problem is if you continually change CPU architectures, > operating systems, etc., during the running of the 'full_analysis.py' > script. It should be fine though if the same diffusion tensor is > optimised on the same machine. > > Cheers, > > Edward > > > On 12/2/06, Sebastien Morin <[EMAIL PROTECTED]> wrote: > >> Hi >> >> I used the full_analysis.py script until convergence for the 4 diffusion >> models (sphere, prolate, oblate, ellipsoid), each on one different >> computer. Those computer, however, are quite similar, all 32-bits x86 >> Gentoo Linux with same kernel, gcc, python, etc. >> >> For the final run, I switched on a different system, our dual core >> pseudo 64-bits NMR console computer running Red Hat Enterprise 4 with >> almost everything different from our Gentoo workstations which are >> really more up-to-date. Before starting the final run, I wanted to check >> if number rounding would be the same... Well, is wasn't and the run with >> the ellipsoid diffusion model ended up saying it wasn't converged yet : >> >> ##################### >> # Convergence tests # >> ##################### >> Chi-squared test: >> chi2 (k-1): 7022.7261139599996 >> chi2 (k): 7022.7261139563052 >> The chi-squared value has not converged. >> Identical model-free models test: >> The model-free models have converged. >> Identical parameter test: >> Spin system: 26 PHE >> Parameter: S2f >> Value (k-1): 0.84811676720047557 >> Value (k): 0.84811676720047491 >> The model-free parameters have not converged. >> Convergence: >> [ No ] >> >> As is obvious, the differences are really small, but still relax thinks >> it's enough to spend many hours more trying to get absolute reproducibility. >> >> My question. >> >> Is it really necessary to get convergence on so small digits ? Probably >> yes, as it was designed this way... So, if yes, why ? Isn't it a problem >> for multi-computer processing ? >> >> Thanks ! >> >> >> Séb :) >> >> >> _______________________________________________ >> 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 > > End of relax-users Digest, Vol 8, Issue 3 > ***************************************** > -- Dr. Daniel Perez Inst. f. Molekularbiologie u. Biophysik Schafmattstr. 20 ETH-Hönggerberg, HPK G 5 CH-8093 Zürich Phone: +41 44 633 25 37 _______________________________________________ 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
