[us-commits] [ehb54/ultrascan3] be9437: Complete the SAXS excluded volume fix: 31 further ...

[emre brookes]

  Branch: refs/heads/ehb54-issue-976
  Home:   https://github.com/ehb54/ultrascan3
  Commit: be9437cf7e072474c7e06337c0716df2ad1d3c34
      https://github.com/ehb54/ultrascan3/commit/be9437cf7e072474c7e06337c0716df2ad1d3c34
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new

  Log Message:
  -----------
  Complete the SAXS excluded volume fix: 31 further rows in somo.atom

Extends the O2H1 correction to every other row carrying the same mistake.

Throughout somo.atom a hybrid's excluded volume is the bare heavy-atom value
plus 5.15 A^3 per attached hydrogen, 5.15 being hydrogen's own excluded volume
in somo.saxs_atoms. These 31 rows carried the bare value despite the hybrid
having hydrogens, i.e. the hydrogen contribution was omitted:

  C4H3  16.44 -> 31.89  x20   C13 C15 C1Q C1R C1T C1U C2 C20 C22 C25 C28
                              C2A C3 C35 C36 C38 C3P C4 C42 C5
  C4H2  16.44 -> 26.74  x8    C14 C15 C16 C17 C18 C19 C1P C21
  C3H2  16.44 -> 26.74  x2    CBB CBC
  C4H1  16.44 -> 21.59  x1    C40

With the four O2H1 rows already corrected earlier on this branch, all 35 rows
of this error class are now consistent. The number of hybrids carrying more
than one excluded volume drops from 6 to 2.

Four rows deviate from the rule in some other way and are deliberately left
untouched, since they need a judgement call rather than arithmetic:

  SG   S2H1   25.1   rule gives 25.01  - looks like a dropped digit, but the
                                         effect is negligible either way
  NE2  N3H1+  12.79  rule gives  7.64  - carries the two-hydrogen value while
                                         its mass 15.02 says one hydrogen
  B    B4H0    2.14  rule gives 29.65  - 2.14 is boron's volume in
                                         somo.saxs_atoms; B1/B2 use 29.65
  OW   O2H2   24     rule gives 19.43  - water oxygen; 24 may well be
                                         deliberate for explicit water

Affects the excluded-volume term in SAXS curve computation for structures
containing these atom names.

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



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