[us-commits] [ehb54/ultrascan3] 9506dc: Correct the record on the vbar ionisation design

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9506dc6c65cc9843842ee92c23626e26543bc5c0
      https://github.com/ehb54/ultrascan3/commit/9506dc6c65cc9843842ee92c23626e26543bc5c0
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-08 (Sat, 08 Aug 2026)

  Changed paths:
    M us_somo/develop/perceiver/DECISIONS.md

  Log Message:
  -----------
  Correct the record on the vbar ionisation design

An earlier note inferred that the identical vbar for the protonated and
deprotonated states meant the stored values already absorbed whatever
ionisation the underlying measurements carried. Mattia has corrected this: the
amino acid vbar values were recalculated by him at pH 7, and setting the
ionised value equal to the base is a deliberate statement that at pH 7 the
volume does not change.

There is also no stored "pH 7 value" anywhere. SOMO derives the species
fractions at run time from the stored pKa by Henderson-Hasselbalch, in
basic_fractions(), and mixes the base and ionised values by those fractions.
For aspartate at pH 7 that is 99.95% deprotonated, which is why the runtime
hydration is effectively the fully ionised value. The field described earlier
as "the pH 7 one" is the fully ionised one; pH 7 merely sits almost entirely
at that end.

This also reframes arginine. Its 0.698 is Mattia's recalculated pH 7 value,
which he states is better than the published sets, so the calculation being
16% high means it is reproducing a published-style number while the reference
is deliberately better than those, rather than the reference being uncertain.

The decision to leave the electrostriction option off is unchanged, and so is
the measurement behind it. Only the explanation changes: the correction
overshoots relative to a recalculated pH 7 reference.

What this confirms is that the implemented design is the intended one. Work at
pH 7 for a non-coded residue, since its pKa cannot be known, and assume the
hydrations determined for the amino acids, every carboxyl deprotonated and
every amine protonated. That is what the hydration rules already do.

Refs ehb54/ultrascan-tickets#980

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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