[us-commits] [ehb54/ultrascan3] 53f39f: Fix deoxynucleotide C2' hybridization: C4H1 -> C4H2

[emre brookes]

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 53f39f42b231277e413ace83e548826caa3ab7a4
      https://github.com/ehb54/ultrascan3/commit/53f39f42b231277e413ace83e548826caa3ab7a4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

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

  Log Message:
  -----------
  Fix deoxynucleotide C2' hybridization: C4H1 -> C4H2

Deoxyribose C2' is bonded to C1', C3' and two hydrogens, so it is a CH2
(C4H2, 14.03). It was typed C4H1 (13.02), the ribose value, where C2'
carries O2' and only one hydrogen.

The deoxy blocks were created by copying the corresponding ribo block and
deleting the O2' atom line, but C2' was never retyped. Every deoxy residue
therefore came out 1.01 Da light, and since residue mass is the sum of its
atom hybrid masses, the error propagated into MW, vbar-weighted quantities
and bead masses for every DNA run.

Corrected in all 22 affected blocks (DA/DC/DG/DT, both the primed and the
starred atom-naming variants, with and without phosphate). Each deoxy
residue is now exactly 16.00 Da below its ribo counterpart, i.e. the loss
of one oxygen and nothing else; previously the gap was 17.01 Da:

  A ->DA   266.27 -> 250.27  (-16.00, was -17.01)
  C ->DC   242.24 -> 226.24  (-16.00, was -17.01)
  G ->DG   282.27 -> 266.27  (-16.00, was -17.01)
  U ->DT   243.22 -> 241.25  (-1.97 = -O +CH2, was -2.98)

Ribose C2' (A/C/G/U, and sugars such as LMT) is untouched.

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


  Commit: 4ae31a8922b1bca3ae30d07dd6f66d2b5ac7c3bb
      https://github.com/ehb54/ultrascan3/commit/4ae31a8922b1bca3ae30d07dd6f66d2b5ac7c3bb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new
    M us_somo/etc/somo.hybrid.new
    M us_somo/etc/somo.residue.new
    M us_somo/etc/somo.saxs_atoms.new

  Log Message:
  -----------
  Add molybdenum cluster support to the SOMO parameter files

Adopts the additive part of Mattia's updated parameter files: support for
polyoxomolybdate clusters, which previously could not be typed at all.

  somo.hybrid      O2H02- (oxide O2-), MO+5, MO+6
  somo.atom        MO1-MO6 as MO+6, MO7/MO8 as MO+5; O2H02- oxide, O2H2
                   water and further O1H0 entries for the O1-O27 cluster
                   oxygens (38 rows)
  somo.saxs_atoms  Cromer-Mann form factors for MO+5 and MO+6, both the
                   9- and 11-parameter variants, matching the MO+3 rows
  somo.residue     two new residues, Molybdenum Cluster Subunit 1 (MO2)
                   and Subunit 2 (MO6)

Purely additive - no existing row is modified, so no current result can
change. Verified: every hybrid referenced by somo.residue resolves in
somo.hybrid; every (atom name, hybrid) pair used by the two new residues
exists in somo.atom; and the new electron counts are correct for Z minus
formal charge (O2- 10, MO+5 37, MO+6 36).

Mattia's copy of somo.residue predates 78465e20, so it is missing glucose;
GLC is deliberately retained here and only his new blocks were taken.

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


  Commit: b112dfd5c5fe820c5ddbac261d394c8ea900d844
      https://github.com/ehb54/ultrascan3/commit/b112dfd5c5fe820c5ddbac261d394c8ea900d844
  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:
  -----------
  Fix SAXS excluded volume for four hydroxyl entries in somo.atom

O10, O1A, O1B and O1N carried 9.13 A^3 as their O2H1 excluded volume, the
value belonging to a bare oxygen (O1H0/O2H0), rather than the 14.28 A^3 used
by every other hydroxyl. The four rows sit directly below O1H0/O2H0 rows for
the same atom names, so this reads as a copy-paste slip.

All 43 O2H1 rows in the file now use 14.28; before this change 39 did and
these 4 did not. Affects the excluded-volume term in SAXS curve computation
for structures containing those atom names.

>From Mattia's updated parameter files.

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


  Commit: 1f0b373b0887e359bf2dd08e7ef193f0800b2f56
      https://github.com/ehb54/ultrascan3/commit/1f0b373b0887e359bf2dd08e7ef193f0800b2f56
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

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

  Log Message:
  -----------
  Fix NDP ionized-state vbar: 0.599 -> 0.589

NADPH (NDP) declared vbar 0.589 for the neutral form but 0.599 for both
ionized states. 0.599 is NAD's vbar, and the NDP header otherwise matches
NAD's line, so the two ionized values were carried over when the entry was
copied from NAD.

Every other multi-state residue in the file repeats the same vbar across all
of its protonation states; NDP was the only one of the 20 that did not. It
now uses 0.589 throughout, so vbar no longer jumps by 1.7% as a function of
pH for NADPH-containing models.

>From Mattia's updated parameter files.

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


  Commit: f00f0bfd2facda5de8de10142e040f2c8b2db1e9
      https://github.com/ehb54/ultrascan3/commit/f00f0bfd2facda5de8de10142e040f2c8b2db1e9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

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

  Log Message:
  -----------
  Set MO+3 radius to 0.69, completing the Mo series

Mattia changed the Mo(III) radius from 0.83 to 0.69 A in both somo.atom and
somo.hybrid when adding the MO+5 and MO+6 entries, and has confirmed 0.69 is
the value to use.

This makes the three Mo radii one consistently sourced set: 0.69 (+3), 0.61
(+5) and 0.73 (+6) are Shannon effective ionic radii, six-coordinate for
Mo(III) and Mo(V) and seven-coordinate for Mo(VI). The previous 0.83
corresponds to no standard Mo radius; it entered in 623ce9cc (2020) with the
multi-pKa support files, with no stated source.

Note for anyone reading the table later: the radius rises from +3 to +6
rather than falling, because the Mo(VI) value is seven-coordinate while the
other two are six-coordinate. That is intentional, not a transcription error.

Unlike the rest of this branch this change is not additive. It alters bead
radii, and hence hydrodynamic results, for existing structures containing
Mo(III).

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


  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>


  Commit: bf1c7305fc74d7d30908e9423dea0a3fbc47e195
      https://github.com/ehb54/ultrascan3/commit/bf1c7305fc74d7d30908e9423dea0a3fbc47e195
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new
    M us_somo/etc/somo.hybrid.new
    M us_somo/etc/somo.residue.new
    M us_somo/etc/somo.saxs_atoms.new

  Log Message:
  -----------
  Merge pull request #492 from ehb54/ehb54-issue-976

SOMO parameter files: adopt Mattia's updates and fix deoxynucleotide C2' hybridization


Compare: https://github.com/ehb54/ultrascan3/compare/8fc78be3a6ca...bf1c7305fc74

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