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Original file (SVG file, nominally 520 ×ばつ 333 pixels, file size: 1.15 MB)
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Summary

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

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

I, the copyright holder of this work, hereby publish it under the following licenses:
[画像:GNU head] 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
w:en:Creative Commons
attribution
This file is licensed under the Creative Commons Attribution 4.0 International license.
Attribution:
SNP model by David Eccles (gringer)
You are free:
  • to share – to copy, distribute and transmit the work
  • to remix – to adapt the work
Under the following conditions:
  • attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
https://creativecommons.org/licenses/by/4.0CC BY 4.0 Creative Commons Attribution 4.0 truetrue
You may select the license of your choice.

Captions

DNA sequence variation in a population. A SNP is just a single nucleotide difference in the genome. The upper DNA molecule differs from the lower DNA molecule at a single base-pair location (a G/A polymorphism)

Items portrayed in this file

depicts

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80e2618911371d2da8252d8edc5d36cf8c929c94

File history

Click on a date/time to view the file as it appeared at that time.

Date/TimeThumbnailDimensionsUserComment
current13:07, 8 May 2021 Thumbnail for version as of 13:07, 8 May 2021 520 ×ばつ 333 (1.15 MB)Gringer Update to slightly more accurate 3D model, showing base rings
21:50, 17 December 2014 Thumbnail for version as of 21:50, 17 December 2014 457 ×ばつ 298 (251 KB)Gringer Increase nominal size to something readable
21:46, 17 December 2014 Thumbnail for version as of 21:46, 17 December 2014 120 ×ばつ 80 (244 KB)Gringer Updated to 3D model, different DNA sequence
01:40, 6 July 2007 Thumbnail for version as of 01:40, 6 July 2007 416 ×ばつ 521 (59 KB)Gringer {{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年07月06日 |Author=David Hall (~~
00:56, 6 July 2007 Thumbnail for version as of 00:56, 6 July 2007 471 ×ばつ 521 (59 KB)Gringer {{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年07月06日 |Author=David Hall (~~~) |other_versions= }}

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Width520
Height332.93881

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