Excluding C and N terminus from Isoelectric calculation

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I'm currently trying to calculate the isoelectric value for amino acid sequences, but excluding the N terminus and C terminus from the calculation. I tried running the isoelectric function with a custom .pk file
isoArr{z, 1} = isoelectric(seq, 'PKVals', 'file.pK');
where file.pk is
N_term 0.0
K 10.53
R 12.48
H 6
D 3.86
E 4.25
C 8.33
Y 10.07
C_term 0.0
However, that did not output the correct values, and deleting the Nterm and Cterm lines gave me an error. I was wondering if there was an easy way to exclude both of these from the calculation or if I basically have to write my own isoelectric function.

Answers (1)

Arthur Goldsipe
Arthur Goldsipe on 4 Mar 2022
I think you want to set the N_term and C_term entries to 7.0 rather than 0.0, since 7.0 is the the "neutral" pK value.




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