Editing Propka (section)

=== Example 1 - Mutagenesis analysis - part 1 === 
This script was developed with the intention of making analysis of possible mutants easier. For example, the reactivity of Cysteines in FRET maleimide labelling is determined by the fraction of the Cysteine residue which is negatively charged (C-). This fraction is related to its pKa value and the pH of the buffer: f(C-)=1/(10(pK-pH)+1). So, one would be interested in having the lowest possible pKa value as possible. Ideally lower than the pH of the buffer. To analyse where to make the best mutant in your protein, you could do the following for several residues. We do the mutagenesis in the command line, since we then could loop over the residues in the protein.<br>
So, in a loop with defined residues, this could look like the following code. Note, now we are quite happy for the result log file, since it collects the pka for the mutants. 

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