Diffraction examples: A/B-DNA, α-helix vs coiled coil, β-sheets (silk, cross-β), collagen, polyethylene, cellulose; crystals from the solids

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
15/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Active
Tech stack
c
Domain
data-visualization, documentation

Research direction

Start with the existing General Chemistry > Diffraction examples, the B-DNA and alpha-helix entries, and the B-DNA test that checks layer-line and meridional positions. Each new example needs sourced coordinates, a short note, and a test for its pattern features, and the help page and example count test must be updated. Done means every listed example is added with a checked note and test, with the helical examples waiting on #991.

Written by the indexing model from the issue text.

Description

enhancement

General Chemistry > Diffraction has B-DNA and an α-helix (fibre) and NaCl, KCl, quartz (crystals). Add examples in pairs that differ in one thing, so the pattern's response to structure is visible:

Biomolecules (fibre)

  • A-DNA next to B-DNA (11 vs 10 bp per turn, 2.6 vs 3.4 Å rise, tilted bases): the cross and the meridional reflection move.
  • α-helix (poly-Ala) next to a two-stranded coiled coil (α-keratin): the 5.4 Å layer line of a straight α-helix becomes 5.1 Å for the coiled coil.
  • β-sheet in two orientations: silk (poly(Gly-Ala) antiparallel sheets, strands along the fibre) and amyloid cross-β (strands across the fibre, e.g. the GNNQQNY steric zipper): the 4.7 Å strand spacing and ~10 Å sheet spacing swap between meridian and equator.
  • Collagen triple helix ((Gly-Pro-Hyp)ₙ): the ~2.9 Å meridional reflection, three chains in one helix.

Polymers (fibre)

  • Polyethylene: planar zig-zag, 2.55 Å repeat.
  • Cellulose Iβ: hydrogen-bonded sheets, 10.4 Å repeat.

Crystals (powder, single crystal), from the Molecular and covalent solids topic: ice, urea, sucrose, diamond, graphite (the 002 layer reflection at 3.35 Å against diamond).

Requirements:

  • Coordinates from a named source in each example's note (Arnott fibre models for A/B-DNA; published silk, collagen and cross-β structures; COD for crystals). A model built rather than taken from a deposition says so.
  • The fibre view keeps the finite-model calculation for non-helical fibres (β-sheets) next to the helical transform of #991; the helical examples come after #991.
  • Notes in the short example style (one 'This calculation shows ...' sentence); the pattern features named in the note are checked by a test (layer-line and meridional/equatorial positions, as the B-DNA test does).
  • Help page and the example count test updated.
Dominant language
C
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Forks
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