File:Dna-SNP.svg
![File:Dna-SNP.svg](https://upload.wikimedia.org/wikipedia/commons/thumb/2/2e/Dna-SNP.svg/520px-Dna-SNP.svg.png?20210508130702)
Original file (SVG file, nominally 520 × 333 pixels, file size: 1.15 MB)
Captions
Captions
Summary
[edit]DescriptionDna-SNP.svg |
English: A Single Nucleotide Polymorphism is a change of a nucleotide at a single base-pair location on DNA. Created using OpenSCAD v2021.01 and Inkscape v1.0.2. |
Date | |
Source | Own work |
Author | David Eccles (Gringer) |
Construction process
[edit]This file was derived from a 3D model of DNA, converted to SVG and coloured using David Eccles' STL2SVG script:
type=orig; ~/scripts/stl2svg.pl ./DNA_linear_complete_helix1.stl:330 ./DNA_linear_complete_helix2.stl:200 ./DNA_linear_complete_${type}_A.stl:140 ./DNA_linear_complete_${type}_C.stl:250 ./DNA_linear_complete_${type}_G.stl:90 ./DNA_linear_complete_${type}_T.stl:30 > out_${type}.svg type=mut; ~/scripts/stl2svg.pl ./DNA_linear_complete_helix1.stl:330 ./DNA_linear_complete_helix2.stl:200 ./DNA_linear_complete_${type}_A.stl:140 ./DNA_linear_complete_${type}_C.stl:250 ./DNA_linear_complete_${type}_G.stl:90 ./DNA_linear_complete_${type}_T.stl:30 > out_${type}.svg
The DNA models were then combined and annotated using Inkscape. The DNA backbone for the model is a pentagon extruded over a sine wave using David Eccles' guided path extrude script. The model source file (in OpenSCAD format) is shown below:
use <guided_extrude.scad>; hl = 100; // helix length hp = 33.2; // helix pitch [in angstroms] hr = 10; // helix radius [in angstroms] bbr = 1.5; // backbone radius loops = hl / hp; // random bases //bases = rands(0, 4, ceil(360 * loops / 34.3),1); // *GRINGENE* -- TAA GGN MGN ATH AAY GGN GAR AAY GAR TGA // -- TAA GGC AGG ATC AAC GGC GAG AAC GAG TGA // A = 0; G = 1; C = 2; T = 3 // [different from my usual order, // to simplify the 3D model logic] bases = [3,3,3, 1,1,2, 0,1,1, 0,3,2, 0,0,2, 1,1,2, 1,0,1, 0,0,2, 1,0,1, 3,1,0]; bAng = atan2(sin(120) - sin(0), cos(120) - cos(0)); drawMode = "all"; module lineTo(x1, x2){ hull(){ translate(x1) sphere(r=0.25, $fn=5); translate(x2) sphere(r=0.25, $fn=5); } } backbone_profile = [for(th = [0:72:359]) [bbr*cos(th), bbr*sin(th)*1]]; inc = floor($t * 30); thf = ($t * 30) - inc; h1limit = (360 * loops); h1jump = (360 * loops); helix_1 = [for(th = [(thf*34.3):(34.3/2):h1jump]) [hr * cos(th), hr * sin(th), hl * th / (360 * loops)]]; helix_2 = [for(th = [120:(34.3/2):(360 * loops+120)]) [hr * cos(th), hr * sin(th), hl * (th-120) / (360 * loops)]]; module purine(){ linear_extrude(height=0.75, center=true){ // average hydrogen bond length in water: 1.97 A // https://en.wikipedia.org/wiki/Hydrogen_bond#Structural_details translate([-0.985,0]) // scale: average of C-C and C=C bond length scale(1.435) translate([-2,0]) rotate(12) rotate(18){ rotate(-30) translate([1,0]) circle(r=1, $fn=6); color("blue") rotate(36) translate([-1 / (2*sin(36)),0]) circle(r=1 / (2*sin(36)), $fn=5); } } } module pyrimidine(){ linear_extrude(height=0.75, center=true){ // average hydrogen bond length in water: 1.97 A // https://en.wikipedia.org/wiki/Hydrogen_bond#Structural_details translate([-0.985,0]) scale(1.435) translate([-2, 0]) translate([1,0]) circle(r=1, $fn=6); } } $vpt = [0, 0, 0]; //$vpr = [310, 105, 10]; $vpr = [0, 0, 0]; rotate([310, 105, 130]) translate([0,0,-hl/2]) { if(drawMode == "all" || drawMode == "helix1") color("lightblue") mapExtrude("vertCylinder", backbone_profile, helix_1); if(drawMode == "all" || drawMode == "helix2") color("pink") mapExtrude("vertCylinder", backbone_profile, helix_2); for(thb = [inc:(360 * loops / 34.3 + inc)]) { thi = thb-inc; th = (thi-thf) * 34.3; thisBase = bases[floor(thb%30)]; doPur = (thisBase < 2); // base bond has a -1.2° angle; // not quite sure how to implement that baseFrac = (doPur ? 0.55 : 0.45); baseFInv = 1 - baseFrac; translate([0,0,hl * th / (360 * loops)]) rotate([-1.2,0,0]){ if(drawMode == "all" || drawMode == "helix2") color("pink") lineTo([hr * cos(th)*(baseFrac-0.15) + hr * cos(th+120) * (baseFrac+0.15), hr * sin(th)*(baseFrac-0.15) + hr * sin(th+120) * (baseFrac+0.15)], [hr * cos(th+120), hr * sin(th+120)]); if(th < (h1jump)) if(drawMode == "all" || drawMode == "helix1") color("lightblue") lineTo([hr * cos(th), hr * sin(th)], [hr * cos(th)*(baseFrac+0.15) + hr * cos(th+120) * (baseFrac-0.15), hr * sin(th)*(baseFrac+0.15) + hr * sin(th+120) * (baseFrac-0.15)]); if(drawMode == "all" || (drawMode == "A" && thisBase == 0) || (drawMode == "G" && thisBase == 1) || (drawMode == "C" && thisBase == 2) || (drawMode == "T" && thisBase == 3) ) color((thisBase < 1) ? "green" : (thisBase < 2) ? "gold" : (thisBase < 3) ? "blue" : "red") translate([hr * cos(th)*baseFrac + hr * cos(th+120) * baseFInv, hr * sin(th)*baseFrac + hr * sin(th+120) * baseFInv]) rotate(180 + bAng + th) if(doPur) { purine(); } else { pyrimidine(); }; if(drawMode == "all" || (drawMode == "A" && thisBase == 3) || (drawMode == "G" && thisBase == 2) || (drawMode == "C" && thisBase == 1) || (drawMode == "T" && thisBase == 0) ) if(th < (h1jump)) color((thisBase < 1) ? "red" : (thisBase < 2) ? "blue" : (thisBase < 3) ? "gold" : "green") translate([hr * cos(th)*baseFrac + hr * cos(th+120) * baseFInv, hr * sin(th)*baseFrac + hr * sin(th+120) * baseFInv]) rotate(bAng+th) if(doPur) { pyrimidine(); } else { purine(); }; } } if(drawMode == "all" || drawMode == "helix1") color("lightblue") { translate(helix_1[len(helix_1)-1]) sphere(r=bbr, $fn=5); translate(helix_1[0]) sphere(r=bbr, $fn=5); } if(drawMode == "all" || drawMode == "helix2") color("pink") { translate(helix_2[0]) sphere(r=bbr, $fn=5); translate(helix_2[len(helix_2)-1]) sphere(r=bbr, $fn=5); } }
Licensing
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Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled GNU Free Documentation License.http://www.gnu.org/copyleft/fdl.htmlGFDLGNU Free Documentation Licensetruetrue |
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File history
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Date/Time | Thumbnail | Dimensions | User | Comment | |
---|---|---|---|---|---|
current | 13:07, 8 May 2021 | ![]() | 520 × 333 (1.15 MB) | Gringer (talk | contribs) | Update to slightly more accurate 3D model, showing base rings |
21:50, 17 December 2014 | ![]() | 457 × 298 (251 KB) | Gringer (talk | contribs) | Increase nominal size to something readable | |
21:46, 17 December 2014 | ![]() | 120 × 80 (244 KB) | Gringer (talk | contribs) | Updated to 3D model, different DNA sequence | |
01:40, 6 July 2007 | ![]() | 416 × 521 (59 KB) | Gringer (talk | contribs) | {{Information |Description=A Single Nucleotide Polymorphism is a change of a nucleotide at a single base-pair location on DNA. Created using Inkscape v0.45.1. [modified to remove long tails on DNA] |Source=self-made |Date=2007-07-06 |Author=David Hall (~~ | |
00:56, 6 July 2007 | ![]() | 471 × 521 (59 KB) | Gringer (talk | contribs) | {{Information |Description=A Single Nucleotide Polymorphism is a change of a nucleotide at a single base-pair location on DNA. Created using Inkscape v0.45.1. |Source=self-made |Date=2007-07-06 |Author=David Hall (~~~) |other_versions= }} |
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Height | 332.93881 |