[us-commits] [ehb54/ultrascan3] 8b715d: perceiver: bring the help page up to date

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8b715d0c3744e8b6afbd371165322e84614a3a1b
      https://github.com/ehb54/ultrascan3/commit/8b715d0c3744e8b6afbd371165322e84614a3a1b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-12 (Wed, 12 Aug 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_perceive.html

  Log Message:
  -----------
  perceiver: bring the help page up to date

Seven commits of user-visible change had landed since the page was last touched.
Documents what a reviewer now actually sees:

 - the ionizable columns (Ionized / Ionized hydration / pKa), why they exist -- the
   coded ionizable residues are already stored this way, so an entry written the same
   way lets US-SOMO pick the state by pH -- and which of them are editable.
 - that the proposed pKa is a CONVENTION value from whichever coded residue shares
   the group, not a prediction, with citrate as the cautionary case: all three
   carboxyls proposed at 3.67 where the real values are ~3.13/4.76/6.40.
 - that the pKa is one value per residue, so editing it anywhere changes the entry.
 - RasMol now shows the residue inside the structure with solvent and hydrogens
   removed, centred on the residue.
 - the review box gives its item count and scrolls, one line per atom.
 - Reset this residue, and revisiting an accepted entry.

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



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