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389 lines
6.7 KiB
Markdown
389 lines
6.7 KiB
Markdown
# DNA CAD / 3D-Printable Model Source Survey
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Date: 2026-05-08
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Purpose: identify downloadable DNA structure models that can feed the CAD force
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probe work. This is a source survey, not an endorsement that any model is
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already mechanically valid for load testing.
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## Best Candidates
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### NIH 3D: DNA Segment Based on 1BNA
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Source:
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```text
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https://3d.nih.gov/entries/251
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https://3d.nih.gov/entries/download/251/2
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```
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Why it matters:
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```text
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PDB-based DNA segment
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based on 1BNA
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NIH 3D output includes STL / GLB / WRL / X3D / PNG
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good science-aligned starting point
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```
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Use:
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```text
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baseline scientific DNA segment
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geometry extraction
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comparison against generated 1BNA pipeline
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```
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Hold:
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```text
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likely fragile as a direct mechanical test object unless thickened or embedded
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```
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### NIH 3D: Triplex and Duplex DNA Flexible Model Kits
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Source:
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```text
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https://3d.nih.gov/entries/22792/1
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https://3d.nih.gov/entries/download/22792/1
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```
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Why it matters:
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```text
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flexible kit based on 1BWG and 1BNA
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includes duplex and triplex components
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files include STL plus visualization formats
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explicitly designed as reconfigurable model parts
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```
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Use:
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```text
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best candidate for force-probe style bench tests
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base-pair component load / snap-fit / connector behavior
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duplex versus triplex geometry comparison
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```
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Hold:
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```text
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model page recommends sintered nylon for stacks
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FDM may need rescaling and connector tolerance checks
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```
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### NIH 3D: DNA Playset
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Source:
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```text
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https://3d.nih.gov/entries/259
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```
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Why it matters:
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```text
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35,000,000:1 scale DNA playset
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four nucleotide parts snap together into arbitrary sequences
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mechanically inspectable modular model
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```
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Use:
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```text
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sequence-dependent physical assembly tests
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connector tolerance / load distribution in modular DNA
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```
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Hold:
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```text
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educational scale model, not atomistic force model
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```
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### NIH 3D: Folding DNA Model
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Source:
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```text
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https://3d.nih.gov/entries/3DPX-001475
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```
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Why it matters:
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```text
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modular DNA model that can be extended
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single strands can separate to illustrate base pairing
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includes detailed assembly and FDM printing notes
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```
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Use:
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```text
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strong practical candidate for print-and-measure experiments
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base-pair snap fit
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strand separation
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repeat-unit load path testing
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```
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Hold:
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```text
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pins may break if printed in weak orientation
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model may need scaling and print orientation controls
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```
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### NIH 3D: Flexible ssDNA and ssRNA
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Source:
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```text
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https://3d.nih.gov/entries/8880
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```
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Why it matters:
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```text
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teaching models of ssDNA / ssRNA in stick representation
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uses PDB 1EHZ
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successfully printed using laser sintering / elastomeric material per source
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```
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Use:
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```text
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single-strand flexibility comparison
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material-dependent bend / torsion proxy
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```
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Hold:
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```text
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not a double-helix lattice by itself
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```
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## Secondary Candidates
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### Sketchfab: DNA Stick and Ball Molecular Model
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Source:
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```text
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https://sketchfab.com/3d-models/dna-stick-and-ball-molecular-model-a8d959ad7f6649a784ae9a874ade7826
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```
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Why it matters:
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```text
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downloadable 3D model
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built in ChimeraX from PDB ID 1BNA
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CC Attribution
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good visual / atomistic reference mesh
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```
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Use:
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```text
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visual comparison
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atomistic 1BNA reference
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mesh inspection
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```
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Hold:
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```text
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NoAI restriction noted by source
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high triangle count
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may require repair / thickening for actual printing
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```
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### CGTrader: DNA Double Helix Free 3D Print Model
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Source:
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```text
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https://www.cgtrader.com/free-3d-print-models/miniatures/other/dna-double-helix
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```
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Why it matters:
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```text
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free model
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STL and Rhino 3DM formats
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marked prepared for 3D printing
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```
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Use:
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```text
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decorative / gross double-helix geometry
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possible CAD-editable Rhino route
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```
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Hold:
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```text
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not necessarily PDB-derived
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license and no-AI terms need review before derivative use
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```
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### 3DCADBrowser: B-DNA
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Source:
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```text
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https://www.3dcadbrowser.com/3d-model/b-dna
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```
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Why it matters:
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```text
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B-DNA model
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formats include STL, OBJ, FBX, BLEND, DXF, DWG, and others
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atom spheres identify oxygen, nitrogen, hydrogen, carbon, phosphorus
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```
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Use:
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```text
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format diversity
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CAD import / conversion experiments
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```
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Hold:
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```text
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download terms may require account or credits
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source has spelling/metadata roughness
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verify license before reuse
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```
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### MakerWorld: DNA Double Helix
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Source:
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```text
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https://makerworld.com/en/models/437066-dna-double-helix
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```
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Why it matters:
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```text
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free STL/CAD model
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DNA model with support guidance
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```
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Use:
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```text
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quick print sanity check
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decorative helix comparison
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```
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Hold:
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```text
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CC BY-NC-SA license
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not scientific geometry
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```
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### Printables DNA Tag
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Source:
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```text
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https://www.printables.com/tag/dna
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```
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Why it matters:
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```text
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aggregates many DNA tagged STL models
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includes folding DNA model kit, double helix models, lamps, manipulatives
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```
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Use:
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```text
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candidate discovery
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practical FDM variants
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compare support-free versus supported helix forms
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```
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Hold:
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```text
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tag page contains mixed decorative, educational, and unrelated models
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vet each license and geometry manually
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```
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## Generation Route
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### RCSB PDB / PDB-101 + NIH 3D Workflow
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Sources:
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```text
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https://pdb101.rcsb.org/learn/3d-printing
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https://pdb101-west.rcsb.org/learn/3d-printing/pdb-structures-and-3d-printing
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https://3d.nih.gov/submit
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```
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Why it matters:
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```text
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RCSB PDB provides scientific source structures
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PDB-101 documents 3D printing workflows
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NIH 3D can process PDB / CIF and mesh files
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NIH 3D can export customized GLB or STL
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```
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Recommended structure IDs:
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```text
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1BNA B-DNA dodecamer
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1BWG triplex DNA component in NIH flexible kit
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1EHZ ssDNA / ssRNA teaching model source
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4UN4 Cas9 with target DNA, useful for protein-DNA complex context
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```
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Use:
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```text
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generate our own controlled source mesh from PDB data
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hash PDB input
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hash STL / GLB output
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record conversion parameters
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feed into CAD force-probe receipt
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```
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## Shortlist for the Force-Probe Path
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Best practical order:
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```text
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1. NIH 3D Folding DNA Model
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2. NIH 3D Triplex and Duplex DNA Flexible Model Kits
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3. NIH 3D DNA Playset
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4. NIH 3D DNA Segment Based on 1BNA
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5. Self-generated 1BNA model through NIH 3D or ChimeraX
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```
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Rationale:
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```text
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modular and snap-fit models are better bench objects than fragile atomistic meshes
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scientific 1BNA models are better for geometry truth but may need thickening
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decorative helices are useful as print controls but weak as biological models
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```
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## Failure Rules
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```text
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decorative helix treated as scientific DNA geometry -> hold
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PDB-derived mesh treated as mechanically printable without repair -> hold
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license omitted from candidate selection -> invalid source record
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downloaded STL used without hash / provenance -> invalid receipt
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atomistic visual mesh used as load-bearing model without thickening -> unsafe / invalid
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```
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