Summarium

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);
  }
}

Potestas usoris

I, the copyright holder of this work, hereby publish it under the following licenses:

Licet hoc documentum exscribere vel distribuere vel demutare sub GNU Liberarum Litterarum Licentiae conditionibus in editione 1.2 aut in ulla editione recentiori a Fundatione Liberarum Programmationis Partium publicata; praeterquam Sectiones Immutabiles et Verba Involucra Adversa et Aversa. Licentiae exemplar praesto est in sectione intitulata GNU Free Documentation License.http://www.gnu.org/copyleft/fdl.htmlGFDLGNU Free Documentation Licensetruetrue

This file is licensed under the Creative Commons Attribution 4.0 International license.

Attributio: SNP model by David Eccles (gringer)

Tibi licet:

• communicare – copiare, distribuere et committere hoc opus
• to remix – to adapt the work

His condicionibus:

• attributio – 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

Tibi typum permissionis ligere licet.