Hello All,
Hi. I am a Biochemistry graduate student at Albert Einstein College of Medicine in New York. In a nutshell, I am studying protein-DNA interactions and use origin regularly to fit my experimental data. Importantly. I have recently switched from a UNIX program (NONLIN) to Origin for data fitting. Initially, this was not a problem because I could rewrite my UNIX functions fairly simply into Origin format with 5 total parameters (energy, temperature, hill coefficient, upper limit and lower limit) and one each independent (protein concentration) and dependent variables (fractional saturation). However, I recently have attempted to write a function that contains 2 independent variables, one for the titrated protein concentration and a second for the SITE on the DNA that is being bound by protein(s). I have written the function using the SWITCH command because it is used when more than 2 possibilities are included in a script. My problems are as follows:
1) How do you assign a second independent variable (In this case, SITE)?
2) How do you tell the function to choose which SITE is being occupied when all I have to direct it is specific protein titration data sets?
3) What is missing from the conversion of NONLIN (UNIX) format to the Origin Switch command? Below I have included the NONLIN function followed by my rewritten Switch function.
I can be reached at cloutier@aecom.yu.edu or 718-430-2860. Any help is greatly appreciated and I thank you very much in advance.
Sincerely,
Tim Cloutier
NONLIN:
c**********************************************************************
FUNCTION FX (ANS, X, Y, IERR, N)
c Function for fitting a two-site system with heterologous proteins.
c In this system the binding site for the second protein cannot be
c discerned.
c x(1) is the protein being titrated and x(2) is the protein being held
c constant.
c The multiple data sets being analyzed have are assumed to have been
c individually scaled. The format is x(1) = TBP, x(2) = TF, x(3) =
c site/competency
c ANS(1) = Delta G1
c ANS(2) = Delta G2
c ans(3) = Delta G12
REAL ANS(4),k1,k2,k12,X(3),Z,RT
integer site,comp
RT = ans(4)
k1 = exp(-ans(1)/RT)
k2 = exp(-ans(2)/RT)
k12 = exp(-ans(3)/RT)
site = x(3) / 10.
comp = mod(x(3),10.)
c Binding polynomial
Z = 1 + k1*x(1) + k2*x(2) + k1*k2*k12*x(1)*x(2)
c Binding equations
if(site.eq.1)then
fx = (k1*x(1) + k1*k2*k12*x(1)*x(2)) / Z
elseif(site.eq.2)then
fx = (k2*x(2) + k1*k2*k12*x(1)*x(2)) / Z
endif
RETURN
END
ORIGIN:
/*still need to define site as independent variable somehow*/
site = TBP
RT = 1.98E-3 * (C+273.33);
k1 = exp(-dGT/RT);
k2 = exp(-dG7/RT);
k12 = exp(-dGC/RT);
m = 1 + k1*x1 + k2*x2 + k1*k2*k12*x1*x2;
switch (site) {
case 1:
site = TBP;
y = (k1*x1 + k1*k2*k12*x1*x2) / m;
break;
case 2:
site = B70;
y = (k2*x2 + k1*k2*k12*x1*x2) / m;
break;
};
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switch command and script/function execution
Posted - 04/11/2001 : 7:12:42 PM
