From: Steve Kneizys <spk4@psu.edu> To : rasmb@bbri.harvard.edu Date: Tue, 24 Mar 1998 22:30:29 -0500

On Tue, 24 Mar 1998 15:33:09 -0800, John Philo wrote: ... > >An alternative approach to this multiple minima problem which does NOT >require the ability to separate the contributions of different species, and >the one that I use in work, is to use numerical constraints to impose mass >balance onto the solutions. It turns out that for each data set only one >of the possible solutions is physically realistic, based on the amounts of >each protein that were actually put into the cell. Thus if you can input >into the fitter the initial concentration of each species (or at least >their molar ratios), and then use this information to penalize solutions >which deviate strongly from mass balance, the fitter can avoid the >physically unrealistic minima and converge on a true and unique solution. > This is one of the features I have put into my software. For each data file, I require the molar ratios of each monomer to be given. Then, I have the fitting function use only one 'total' A0 at R0 as a parameter, use that value and the ratios to define the other 'total' concentrations of each monomer, and use the K parameters and mass-balance to solve for the concentrations of each species at R0 using the Newton-Raphson method. The result is that for each iteration of the nonlinear least squares procedure, the mass balance requirement is satisfied. I chose this method because of the success using it with NMR and Calorimetric data. Steve... -- Steve Kneizys (spk4@psu.edu) Graduate Student Department of Biochemistry and Molecular Biology Pennsylvania State University College of Medicine The Milton S. Hershey Medical Center P.O. Box 850 Hershey, PA 17033

Index: [thread] [date] [subject] [author]