Datoteka:Dna-SNP.svg

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Sažetak

OpisDna-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.
Datum	8 maj 2021
Izvor	Vlastito djelo
Autor	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);
  }
}

Licenciranje

Ja, vlasnik autorskog prava ovog djela, ovdje ga objavljujem pod sljedećim licencama:

Dozvoljeno je kopirati, distribuirati i/ili mijenjati ovaj članak pod uslovima navedenim u GNU licenci za slobodnu dokumentaciju, verzija 1.2 ili kasnijom verzijom izdatom od Free Software Foundation; bez nepromjenljivih dijelova, te bez sadržaja na naslovnoj i zadnjoj strani. Kopija licence se nalazi pod poglavljem GNU Free Documentation License.

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

Pripisivanje: SNP model by David Eccles (gringer)

Slobodni ste:

da dijelite – da kopirate, distributirate i prenosite djelo
da remiksate – da prilagodite djelo

Pod sljedećim uslovima:

pripisivanje – Morate pripisati odgovarajuće autorske zasluge, osigurati link ka licenci i naznačiti jesu li napravljene izmjene. To možete uraditi na bilo koji razumni način, ali ne tako da se sugerira da davalac licence odobrava Vas ili Vašu upotrebu njegovog djela.

Možete odabrati licencu po vašem izboru.

Historija datoteke

Kliknite na datum/vrijeme da vidite verziju datoteke iz tog vremena.

	Datum/vrijeme	Dimenzije	Korisnik	Komentar
trenutno	14:07, 8 maj 2021	520 × 333 (1,15 MB)	Gringer	Update to slightly more accurate 3D model, showing base rings
	22:50, 17 decembar 2014	457 × 298 (251 KB)	Gringer	Increase nominal size to something readable
	22:46, 17 decembar 2014	120 × 80 (244 KB)	Gringer	Updated to 3D model, different DNA sequence
	02:40, 6 juli 2007	416 × 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=2007-07-06 \|Author=David Hall (~~
	01:56, 6 juli 2007	471 × 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=2007-07-06 \|Author=David Hall (~~~) \|other_versions= }}

Upotreba datoteke

Sljedeća stranica koristi ovu datoteku:

Jednonukleotidni polimorfizam

Globalna upotreba datoteke

Sljedeći wikiji koriste ovu datoteku:

Upotreba na ar.wikipedia.org
- تعدد أشكال النوكليوتيدات المفردة
- تحليل الجينات
Upotreba na ast.wikipedia.org
- Haplogrupu I-M253
Upotreba na be.wikipedia.org
- Гаплатып
Upotreba na ca.wikipedia.org
- Polimorfisme de nucleòtids simples
- Modelització molecular de l'ADN
- Haplogrup I-M253
Upotreba na cs.wikipedia.org
- Jednonukleotidový polymorfismus
Upotreba na de.wikipedia.org
- DNA-Analyse
- Einzelnukleotid-Polymorphismus
- Genetische Variation (Mensch)
Upotreba na el.wikipedia.org
- Προγεννητικός έλεγχος
Upotreba na en.wikipedia.org
- Single-nucleotide polymorphism
- Haplotype
- Genealogical DNA test
- Human genetic variation
- Haplogroup I-M253
- User:Bci2
- Molecular models of DNA
- User:Bci2/Books/Wk2Book
- User:Bci2/Books/Wk3vol1
- User:Bci2/Books/Wk4
- Talk:Molecular models of DNA/Galleries
- Heather Dewey-Hagborg
- Evolution of the wolf
- Talk:DNA sequencing/Archive 1
Upotreba na es.wikipedia.org
- Polimorfismo de nucleótido único
- Mapa genético de salud
- Evolución del lobo
- Haplogrupo I1 (ADN-Y)
- Variación genética humana
Upotreba na et.wikipedia.org
- Üksiku nukleotiidi polümorfism
- Kasutaja:Dšapoval/SHBG
Upotreba na fa.wikipedia.org
- چندریختی تک‌نوکلئوتید
- فارماکوژنومیک
- پلی مورفیسم تک نوکلئوتیدی
Upotreba na fi.wikipedia.org
- Yhden emäksen monimuotoisuus
Upotreba na fr.wikipedia.org
- Polymorphisme nucléotidique
- Haplogroupe I-M253
- Test ADN généalogique
Upotreba na gl.wikipedia.org
- Polimorfismo dun só nucleótido
Upotreba na he.wikipedia.org
- SNP
Upotreba na hu.wikipedia.org
- Egypontos nukleotid-polimorfizmus
- Haplotípus
Upotreba na it.wikipedia.org
- Aplogruppo I-M253
Upotreba na ja.wikipedia.org
- 一塩基多型
- ゲノム薬理学
- 系統DNA検査
Upotreba na la.wikipedia.org
- Polymorphismus nucleotidi singularis
Upotreba na mk.wikipedia.org
- Хаплотип

Pogledajte globalne upotrebe ove datoteke.

Metapodaci

Ova datoteka sadržava dodatne podatke koje je vjerovatno dodala digitalna kamera ili skener u procesu snimanja, odnosno digitalizacije. Ako je datoteka mijenjana, podaci možda nisu u skladu sa stvarnim stanjem.

Širina	520
Visina	332.93881

Datoteka:Dna-SNP.svg

Sažetak

Construction process

Licenciranje

Captions

Items portrayed in this file

prikazuje

stvaralac

some value

status autorskog prava

zaštićeno autorskim pravima

licenca

GNU Free Documentation License, version 1.2 or later ^engleski

Creative Commons Attribution 4.0 International ^engleski

source of file ^engleski

original creation by uploader ^engleski

datum osnivanja / utemeljenja

18 decembar 2014

media type ^engleski

image/svg+xml

data size ^engleski

1.203.312 Bajt

visina

333 piksel

širina

520 piksel

checksum ^engleski

80e2618911371d2da8252d8edc5d36cf8c929c94

Historija datoteke

Upotreba datoteke

Globalna upotreba datoteke

Metapodaci

Datoteka:Dna-SNP.svg

Sažetak

Construction process

Licenciranje

Captions

Items portrayed in this file

some value

GNU Free Documentation License, version 1.2 or later engleski

Creative Commons Attribution 4.0 International engleski

source of file engleski

original creation by uploader engleski

18 decembar 2014

media type engleski

image/svg+xml

data size engleski

1.203.312 Bajt

333 piksel

520 piksel

checksum engleski

80e2618911371d2da8252d8edc5d36cf8c929c94

Historija datoteke

Upotreba datoteke

Globalna upotreba datoteke

Metapodaci

GNU Free Documentation License, version 1.2 or later ^engleski

Creative Commons Attribution 4.0 International ^engleski

source of file ^engleski

original creation by uploader ^engleski

media type ^engleski

data size ^engleski

checksum ^engleski