[us-commits] [ehb54/ultrascan3] 0eae33: perceiver: whole-protein psv, incumbent table vs D...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0eae330a8adc633820434f82ccb2e4c1e684a152
      https://github.com/ehb54/ultrascan3/commit/0eae330a8adc633820434f82ccb2e4c1e684a152
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-10 (Mon, 10 Aug 2026)

  Changed paths:
    M us_somo/develop/perceiver/Makefile
    A us_somo/develop/perceiver/data/psv/1BEB.pdb
    A us_somo/develop/perceiver/data/psv/2CGA.pdb
    A us_somo/develop/perceiver/data/psv/README.md
    A us_somo/develop/perceiver/data/psv_measured.txt
    A us_somo/develop/perceiver/tests/protein_psv.cpp

  Log Message:
  -----------
  perceiver: whole-protein psv, incumbent table vs D&Z increments vs D&Z+pH7

Mattia's question was whether to substitute somo.residue's amino-acid psv set with
one derived from the atomic volume increments. The residue-level four-way table
localised the differences but could not say which is right; this compares all three
against measured protein psv, using SOMO's own aggregation (calc_vbar_updated).

Measured values mined from Durchschlag Table 5 + the albumin table, taking only the
CORRECTED columns (phi, phi(0), v(0)) -- the apparent columns vary 5.7% at constant
pH purely from cosolvent, so they cannot be compared against a computed value.

Two guards the first run needed:
 - explicit H/D are stripped. D&Z is a united-atom scheme and so is somo.residue
   (ALA: N 15.02, CA 13.02, CB 15.04), so explicit hydrogens double count. The psv
   guard already refused them; the tool must not hand them over in the first place.
 - a structure whose usable residues fall below 95% is EXCLUDED, not reported. Before
   this, 2AAS averaged a handful of surviving residues into a confident-looking
   +13.7%. With H stripped it agrees with 8RAT to four decimals.

All three columns are gated on table membership so they cover identical residues;
otherwise a ligand the table cannot represent (1BEB's SO4) would count for D&Z only.

Co-Authored-By: Claude Opus 5 <noreply at anthropic.com>



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