Hi Ivan, That is quite a strange problem you are seeing, as kex is constrained in NESSY to be positive! It could be a problem of the implementation of parameter constraints. In NESSY, if the constraint is violated, the chi-squared target function value is simply squared. To see this, search for the text "Constraints_container" in the file:
http://svn.gna.org/viewcvs/*checkout*/nessy/nessy/math_fns/models.py?revision=1094&content-type=text%2Fplain It is a bit difficult to tell if this algorithm is the problem though from the little information given. Could you give an example? Are there messages which you could post that are more informative? Cheers. It might be worth trying out different relaxation dispersion software and comparing the results. For example there is the software relax ( http://www.nmr-relax.com) as well as CPMGFit, cpmg_fit, CATIA, GUARDD, ShereKhan, GLOVE and chemex (all listed with download links at http://www.nmr-relax.com/manual/Comparison_dispersion_analysis_software.html). I know that with relax, the powerful logarithmic barrier constraint algorithm ( https://en.wikipedia.org/wiki/Barrier_function#Logarithmic_barrier_function) from minfx (http://gna.org/projects/minfx/) is used for the dispersion analysis, and with that you can never have negative values. The relax manual at http://download.gna.org/relax/manual/relax.pdf has a good comparison of optimisation features of all dispersion software in table 10.3 on page 183. Anyway, to solve the problem, more information would be required. Regards, Edward On 28 March 2014 22:09, Ivan Corbeski <[email protected]>wrote: > Dear Sir or Madam, > > I have noticed that NESSY often gives out negative kex and phi values for > residues with obviously perfect dispersion curves. Why is that and what > does that mean? Is there a way to overcome that problem? > > Yours sincerely, > > Ivan Corbeski > Goethe University Frankfurt, Germany > Max-von-Laue Str. 9, 60438 Frankfurt/Main > Email: [email protected] > > > > _______________________________________________ > Nessy-users mailing list > [email protected] > https://mail.gna.org/listinfo/nessy-users >
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