[us-commits] [ehb54/ultrascan3] 0cc99d: Measure pH 7 ionisation for psv, and leave it off

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0cc99de22997c68505e8b2b6f42da3c38db7de0b
      https://github.com/ehb54/ultrascan3/commit/0cc99de22997c68505e8b2b6f42da3c38db7de0b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-08 (Sat, 08 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_psv.h
    M us_somo/develop/perceiver/DECISIONS.md
    M us_somo/develop/perceiver/tests/psv.cpp
    M us_somo/develop/src/us_hydrodyn_psv.cpp

  Log Message:
  -----------
  Measure pH 7 ionisation for psv, and leave it off

The pH 7 assumption transformed hydration, so the same reasoning was applied
to partial specific volume: charge the carboxyl as a carboxylate, protonate
the guanidinium, and take an electrostriction term for each. Implemented as an
option and measured against the stored values.

The measurement says not to use it. Aspartate moves from 1.3% low to 11.0%
low, glutamate from 1.2% to 9.0%, while arginine improves from 15.9% high to
9.7%. Mean absolute error goes from 6.23% to 9.05%: a clear net loss.

The reason the symmetry with hydration breaks is visible in the residue table.
It lists the same vbar for the protonated and deprotonated state of every
ionisable residue, so ionisation there changes mass, radius, protons and
hydration but never volume. Those values descend from densitometry on real
amino acids at neutral pH and already contain whatever ionisation was present,
whereas the Durchschlag and Zipper electrostriction is an explicit correction
to a neutral-basis increment sum. Applying both counts it twice.

Hydration was different precisely because the table does carry two hydration
numbers per ionisable atom, with the pH 7 value in its own field. There the
assumption had a ground truth to match, and matching it took hydration from
48% to 94% of residue types within half a water.

The option stays, off by default, with the measured numbers in the header
comment and a test that asserts the default is whichever setting actually
measures better. If the reference values are ever placed on a single stated
ionisation basis, flipping it will be a one-line change and the test will
report whether it helped.

This does not explain arginine, which is still 15.9% high untouched and 9.7%
high with electrostriction. It is the known outlier of the scheme: the six
published residue-volume sets in Perkins 1986 disagree with each other about
arginine by 17%.

Refs ehb54/ultrascan-tickets#980

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



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