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<H2><A NAME="SECTION00091000000000000000">
New ion species</A>
</H2>
<P>
MELTING is currently using the algorithm from Owczarzy et al, 2008 (see the MELTING documentation
for the complete reference.)to correct the computed melting temperature depending on the ion
concentrations. This algorithm can take into account the effect of monovalent cations and one divalent
cation : the magnesium.
<BR>
<BR><SPAN CLASS="textbf">1)</SPAN> If the new ion species can be integrated into the algorithm of Owczarzy et al, 2008, you have to change
the method <SPAN CLASS="textit">public CorrectionMethod getIonCorrectionMethod (Environment environment)</SPAN> of the
RegisterMethods class in the melting.configuration package. Otherwise, you must report to the following
section for <SPAN CLASS="textit">new denaturing agents</SPAN> even thought the new species is not a denaturing agent.
<P>
<PRE>
public CorrectionMethod getIonCorrectionMethod
(Environment environment){
// A specific ion correction is required by the user.
if (environment.getOptions().containsKey
(OptionManagement.ionCorrection)){
[...]
}
// No specific ion correction is required, the
// algorithm from Owczarzy et al, 2008 will now be
// used. You have to include your new ion species
// here.
else{
// If it is a new monovalent cation, you must change
// the monovalent concentration.
double monovalent = environment.getNa() + environment.getK()
+ environment.getTris() / 2
+ environment.getNewSpecies();
[...]
// Here are the important variable you may have to
// change to integrate your new ion species (if it
// is a divalent cation or other ion and you know a
// relationship between magnesium concentration and
// this new ion species.)
double Mg = environment.getMg() - environment.getDNTP();
double ratio = Math.sqrt(Mg) / monovalent;
[...]
}
}
</PRE>
<P>
<SPAN CLASS="textbf">2)</SPAN> If you know a relationship between your new ion species and Na, Mg, Tris or K, don't forget
to add your new ion species in the different classes computing a sodium equivalence in the
melting.ionCorrection.SodiumEquivalent package.
You will have to change the following methods :
<P>
In the different classes from the melting.ionCorrection.SodiumEquivalent package.
<PRE>
public double computeSodiumEquivalent(double Na, double Mg,
double K,double Tris, double dNTP, double newSpecies) {
// Change the base implementation in the SodiumEquivalent
// class too.
double NaEq = super.getSodiumEquivalent(Na, Mg, K, Tris,
dNTP, double newSpecies, parameter);
[...]
return NaEq;
}
</PRE>
<P>
In the SodiumEquivalentMethod interface from the melting.methodInterfaces package.
<PRE>
public double computeSodiumEquivalent(double Na, double Mg,
K, double Tris, double dNTP, double newSpecies);
</PRE>
<P>
In the ApproximativeMode class from the melting.approximativeMethods
<PRE>
public void setUpVariables(HashMap<String, String> options) {
this.environment = new Environment(options);
if (isNaEqPossible()){
if (environment.getMg() > 0 || environment.getK() > 0
|| environment.getTris() > 0
|| environment.getNewSpecies() > 0){
[...]
}
[...]
}
[...]
}
</PRE>
<P>
In the Helper class from the melting package
<PRE>
public static double computesNaEquivalent(Environment
environment){
double NaEq = environment.getNa() + environment.getK()
+ environment.getTris() / 2
+ environment.getNewSpecies();
[...]
}
</PRE>
<P>
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<ADDRESS>
Computational Neurobiology
2009-08-24
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