[us-commits] [ehb54/ultrascan3] b5bf19: perceiver: record the measured accuracy in the hel...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b5bf19ba94beecb295a75f2c1400dcdc03ba1cd7
      https://github.com/ehb54/ultrascan3/commit/b5bf19ba94beecb295a75f2c1400dcdc03ba1cd7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-09 (Sun, 09 Aug 2026)

  Changed paths:
    M us_somo/develop/perceiver/GUI_TESTING.md
    M us_somo/somo/doc/manual/somo/somo_perceive.html

  Log Message:
  -----------
  perceiver: record the measured accuracy in the help page

The help page said what each computed number is worth in general terms.
Now there are numbers, from residues where the answer is known: rename a
residue the table already codes, leave its atoms untouched, and the coded
entry becomes the answer key.

  really  psv perceived/coded    volume perceived/coded   hydration
  SER     0.632 / 0.628  +0.6%   97.95 /  95.40  +2.7%    2.0 / 2.0
  LEU     0.892 / 0.898  -0.7%  158.61 / 164.00  -3.3%    1.0 / 1.0
  LYS     0.871 / 0.818  +6.5%  172.85 / 167.30  +3.3%    4.0 / 4.0
  ARG     0.809 / 0.698 +15.9%  196.19 / 194.00  +1.1%    3.0 / 3.0

Hydration was exact on all four -- the quantity with the least theoretical
backing, and the one a tester is most able to sanity-check. Volume within
+-3.3%. psv splits by charge: neutral side chains +-0.7%, charged ones high.
The arginine +15.9% is reproduced independently by the isolated-residue
validation and matches the reading that the tabulated Arg psv was measured
unprotonated while the increments assume protonation -- so the help page
tells the user to treat a perceived psv for a charged group as provisional.

Chain embedding caused no difficulty: one non-coded residue, three in a row
and three alternating with coded ones gave identical values and built
cleanly (244/242/242 beads). The residuals track charge, not chain context
-- the opposite of what was expected, since the perceiver sees the real
bonded neighbours and so perceives backbone N and C as amide and carbonyl.

Same table added to the GUI cheat sheet, with the three new test files.



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