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DetectorConstruction.cc
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24 // ********************************************************************
25 //
26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained using the Geant4-DNA software
28 // and the DNA geometry given in the Geom_DNA example
29 // shall cite the following Geant4-DNA collaboration publications:
30 // [1] NIM B 298 (2013) 47-54
31 // [2] Med. Phys. 37 (2010) 4692-4708
32 // The Geant4-DNA web site is available at http://geant4-dna.org
33 //
36 
37 #include "DetectorConstruction.hh"
38 
39 // Geant4
40 #include "globals.hh"
41 #include "CLHEP/Units/SystemOfUnits.h"
42 #include "G4LogicalVolume.hh"
43 #include "G4UnionSolid.hh"
44 #include "G4Box.hh"
45 #include "G4Orb.hh"
46 #include "G4Tubs.hh"
47 #include "G4Ellipsoid.hh"
48 #include "G4PVParameterised.hh"
49 #include "G4PVPlacement.hh"
50 #include "G4RotationMatrix.hh"
51 #include "G4VisAttributes.hh"
52 #include "G4NistManager.hh"
53 #include "ChromosomeParameterisation.hh"
54 
55 #define countof(x) (sizeof(x) / sizeof(x[0]))
56 
57 using namespace std;
58 using CLHEP::mm;
59 using CLHEP::degree;
60 using CLHEP::nanometer;
61 using CLHEP::micrometer;
62 
63 static G4VisAttributes visInvBlue(false, G4Colour(0.0, 0.0, 1.0));
64 static G4VisAttributes visInvWhite(false, G4Colour(1.0, 1.0, 1.0));
65 static G4VisAttributes visInvPink(false, G4Colour(1.0, 0.0, 1.0));
66 static G4VisAttributes visInvCyan(false, G4Colour(0.0, 1.0, 1.0));
67 static G4VisAttributes visInvRed(false, G4Colour(1.0, 0.0, 0.0));
68 static G4VisAttributes visInvGreen(false, G4Colour(0.0, 1.0, 0.0));
69 static G4VisAttributes visBlue(true, G4Colour(0.0, 0.0, 1.0));
70 static G4VisAttributes visWhite(true, G4Colour(1.0, 1.0, 1.0));
71 static G4VisAttributes visPink(true, G4Colour(1.0, 0.0, 1.0));
72 static G4VisAttributes visCyan(true, G4Colour(0.0, 1.0, 1.0));
73 static G4VisAttributes visRed(true, G4Colour(1.0, 0.0, 0.0));
74 static G4VisAttributes visGreen(true, G4Colour(0.0, 1.0, 0.0));
75 
76 
77 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
78 
79 DetectorConstruction::DetectorConstruction() :
80  G4VUserDetectorConstruction(),
81  fBuildChromatineFiber(true),
82  fBuildBases(false)
83 {
84 }
85 
86 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
87 
88 DetectorConstruction::~DetectorConstruction()
89 {
90 }
91 
92 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
93 
94 G4VPhysicalVolume* DetectorConstruction::Construct()
95 {
96  DefineMaterials();
97  return ConstructDetector();
98 }
99 
100 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
101 
102 void DetectorConstruction::DefineMaterials()
103 {
104  // Water is defined from NIST material database
105  G4NistManager *man = G4NistManager::Instance();
106  man->FindOrBuildMaterial("G4_WATER");
107 }
108 
109 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
110 
111 void DetectorConstruction::LoadChromosome(const char* filename,
112  G4VPhysicalVolume* chromBox,
113  G4LogicalVolume* logicBoxros)
114 {
115  ChromosomeParameterisation* cp = new ChromosomeParameterisation(filename);
116  new G4PVParameterised("box ros",
117  logicBoxros,
118  chromBox,
119  kUndefined,
120  cp->GetNumRosettes(),
121  cp);
122 
123  G4cout << filename << " done" << G4endl;
124 }
125 
126 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
127 
128 G4VPhysicalVolume* DetectorConstruction::ConstructDetector()
129 {
130  if(fBuildBases == false && fBuildChromatineFiber == false)
131  {
132  G4cout <<"======================================================" << G4endl;
133  G4cout <<"WARNING from DetectorConstruction::ConstructDetector:" << G4endl;
134  G4cout << "As long as the flags fBuildBases and fBuildChromatineFiber are "
135  "false, the output root file will be empty" << G4endl;
136  G4cout << "This is intended for fast computation, display, testing ..."
137  << G4endl;
138  G4cout <<"======================================================" << G4endl;
139  }
140 
141  G4String name;
142 
143  /***************************************************************************/
144  // World
145  /***************************************************************************/
146 
147  DefineMaterials();
148  G4Material* waterMaterial = G4Material::GetMaterial("G4_WATER");
149 
150  G4Box* solidWorld = new G4Box("world", 10.0 * mm, 10.0 * mm, 10.0 * mm);
151  G4LogicalVolume* logicWorld = new G4LogicalVolume(solidWorld,
152  waterMaterial,
153  "world");
154  G4PVPlacement* physiWorld = new G4PVPlacement(0,
155  G4ThreeVector(),
156  "world",
157  logicWorld,
158  0,
159  false,
160  0);
161  logicWorld->SetVisAttributes(&visInvWhite);
162 
163  /****************************************************************************/
164  // Box nucleus
165  /****************************************************************************/
166 
167  G4Box* solidTin = new G4Box("tin",
168  13 * micrometer,
169  10 * micrometer,
170  5 * micrometer);
171  G4LogicalVolume* logicTin = new G4LogicalVolume(solidTin,
172  waterMaterial,
173  "tin");
174  G4VPhysicalVolume* physiTin = new G4PVPlacement(0,
175  G4ThreeVector(),
176  "tin",
177  logicTin,
178  physiWorld,
179  false,
180  0);
181  logicTin->SetVisAttributes(&visInvWhite);
182 
183  /****************************************************************************/
184  // Cell nucleus
185  /****************************************************************************/
186 
187  G4Ellipsoid* solidNucleus = new G4Ellipsoid("nucleus",
188  11.82 * micrometer,
189  8.52 * micrometer,
190  3 * micrometer,
191  0,
192  0);
193  G4LogicalVolume* logicNucleus = new G4LogicalVolume(solidNucleus,
194  waterMaterial,
195  "logic nucleus");
196  G4VPhysicalVolume* physiNucleus = new G4PVPlacement(0,
197  G4ThreeVector(),
198  "physi nucleus",
199  logicNucleus,
200  physiTin,
201  false,
202  0);
203  logicNucleus->SetVisAttributes(&visPink);
204 
205  /****************************************************************************/
206  // Chromosomes territories
207  /****************************************************************************/
208  // NOTE: The only supported values for the rotation are
209  // 0 and 90 degrees on the Y axis.
210  G4double chromosomePositionSizeRotation[][7] = {
211  {4.467, 2.835, 0, 1.557, 1.557, 1.557, 90},
212  {-4.467, 2.835, 0, 1.557, 1.557, 1.557, 0},
213  {4.423, -2.831, 0, 1.553, 1.553, 1.553, 90},
214  {-4.423, -2.831, 0, 1.553, 1.553, 1.553, 0},
215  {1.455, 5.63, 0, 1.455, 1.455, 1.455, 0},
216  {-1.455, 5.63, 0, 1.455, 1.455, 1.455, 90},
217  {1.435, 0, 1.392, 1.435, 1.435, 1.435, 0},
218  {-1.435, 0, 1.392, 1.435, 1.435, 1.435, 90},
219  {1.407, 0, -1.450, 1.407, 1.407, 1.407, 90}, // 5 right
220  {-1.407, 0, -1.450, 1.407, 1.407, 1.407, 0}, // 5 left
221  {1.380, -5.437, 0, 1.380, 1.380, 1.380, 0},
222  {-1.380, -5.437, 0, 1.380, 1.380, 1.380, 90},
223  {1.347, 2.782, -1.150, 1.347, 1.347, 1.347, 90},
224  {-1.347, 2.782, -1.150, 1.347, 1.347, 1.347, 0},
225  {1.311, -2.746, -1.220, 1.311, 1.311, 1.311, 90},
226  {-1.311, -2.746, -1.220, 1.311, 1.311, 1.311, 0},
227  {7.251, -2.541, 0, 1.275, 1.275, 1.275, 0},
228  {-6.701, 0, -0.85, 1.275, 1.275, 1.275, 90},
229  {4.148, 0, 1.278, 1.278, 1.278, 1.278, 90}, // 10 right
230  {-4.148, 0, 1.278, 1.278, 1.278, 1.278, 0}, // 10 left
231  {4.147, 0, -1.277, 1.277, 1.277, 1.277, 0},
232  {-4.147, 0, -1.277, 1.277, 1.277, 1.277, 90},
233  {8.930, 0.006, 0, 1.272, 1.272, 1.272, 90},
234  {-7.296, 2.547, 0, 1.272, 1.272, 1.272, 90},
235  {1.207, -2.642, 1.298, 1.207, 1.207, 1.207, 0},
236  {-1.207, -2.642, 1.298, 1.207, 1.207, 1.207, 90},
237  {1.176, 2.611, 1.368, 1.176, 1.176, 1.176, 0},
238  {-1.176, 2.611, 1.368, 1.176, 1.176, 1.176, 90},
239  {4.065, 5.547, 0, 1.155, 1.155, 1.155, 90}, // 15 right
240  {-4.065, 5.547, 0, 1.155, 1.155, 1.155, 0}, // 15 left
241  {6.542, 0.159, 1.116, 1.116, 1.116, 1.116, 0},
242  {-9.092, 0, 0, 1.116, 1.116, 1.116, 0},
243  {6.507, 0.159, -1.081, 1.081, 1.081, 1.081, 90},
244  {-7.057, -2.356, 0, 1.081, 1.081, 1.081, 90},
245  {3.824, -5.448, 0, 1.064, 1.064, 1.064, 90},
246  {-3.824, -5.448, 0, 1.064, 1.064, 1.064, 0},
247  {5.883, -5.379, 0, 0.995, 0.995, 0.995, 0},
248  {-9.133, -2.111, 0, 0.995, 0.995, 0.995, 0},
249  {6.215, 5.387, 0, 0.995, 0.995, 0.995, 0}, // 20 right
250  {-6.971, -4.432, 0, 0.995, 0.995, 0.995, 90}, // 20 left
251  {9.583, 2.177, 0, 0.899, 0.899, 0.899, 90},
252  {-9.467, 2.03, 0, 0.899, 0.899, 0.899, 0},
253  {9.440, -2.180, 0, 0.914, 0.914, 0.914, 90},
254  {-6.34, 0, 1.339, 0.914, 0.914, 0.914, 0},
255  {-6.947, 4.742, 0, 0.923, 0.923, 0.923, 90}, // Y
256  {7.354, 2.605, 0, 1.330, 1.330, 1.330, 0} // X
257  };
258 
259  G4RotationMatrix* rotch = new G4RotationMatrix;
260  rotch->rotateY(90 * degree);
261 
262  vector<G4VPhysicalVolume*> physiBox(48);
263 
264  for (unsigned int i = 0; i < countof(chromosomePositionSizeRotation); i++)
265  {
266  G4double* p = &chromosomePositionSizeRotation[i][0];
267  G4double* size = &chromosomePositionSizeRotation[i][3];
268  G4double rotation = chromosomePositionSizeRotation[i][6];
269  G4ThreeVector pos(p[0] * micrometer, p[1] * micrometer, p[2] * micrometer);
270  G4RotationMatrix* rot = rotation == 0 ? 0 : rotch;
271 
272  ostringstream ss;
273  ss << "box" << (i / 2) + 1 << (i % 2 ? 'l' : 'r');
274  name = ss.str();
275  ss.str("");
276  ss.clear();
277 
278  /*
279  snprintf(name, countof(name), "box%d%c",
280  (i / 2) + 1, i % 2 ? 'l' : 'r');
281  */
282  G4Box* solidBox = new G4Box(name,
283  size[0] * micrometer,
284  size[1] * micrometer,
285  size[2] * micrometer);
286  G4LogicalVolume* logicBox = new G4LogicalVolume(solidBox,
287  waterMaterial,
288  name);
289  physiBox[i] = new G4PVPlacement(rot,
290  pos,
291  "chromo",
292  logicBox,
293  physiNucleus,
294  false,
295  0);
296  logicBox->SetVisAttributes(&visBlue);
297  }
298 
299  /**************************************************************************/
300  // Box containing the chromatin flowers
301  /**************************************************************************/
302 
303  G4Tubs* solidBoxros = new G4Tubs("solid box ros",
304  0 * nanometer,
305  399 * nanometer,
306  20 * nanometer,
307  0 * degree,
308  360 * degree);
309  G4LogicalVolume* logicBoxros = new G4LogicalVolume(solidBoxros,
310  waterMaterial,
311  "box ros");
312  logicBoxros->SetVisAttributes(&visInvBlue);
313 
314  //Loading flower box position for each chromosome territory
315 
316  for (int k = 0; k < 22; k++)
317  {
318  ostringstream oss;
319  oss << "chromo" << k + 1 << ".dat";
320  name = oss.str();
321  oss.str("");
322  oss.clear();
323  //snprintf(name, countof(name), "chromo%d.dat", k + 1);
324  LoadChromosome(name.c_str(), physiBox[k * 2], logicBoxros);
325  LoadChromosome(name.c_str(), physiBox[k * 2 + 1], logicBoxros);
326  }
327 
328  LoadChromosome("chromoY.dat", physiBox[44], logicBoxros);
329  LoadChromosome("chromoX.dat", physiBox[45], logicBoxros);
330 
331  /****************************************************************************/
332  if (fBuildChromatineFiber)
333  {
334  // chromatin fiber envelope
335  G4Tubs* solidEnv = new G4Tubs("chromatin fiber",
336  0,
337  15.4 * nanometer,
338  80.5 * nanometer,
339  0 * degree,
340  360 * degree);
341  G4LogicalVolume* logicEnv = new G4LogicalVolume(solidEnv,
342  waterMaterial,
343  "LV chromatin fiber");
344  logicEnv->SetVisAttributes(&visInvPink);
345 
346  // Chromatin fiber position
347  for (G4int i = 0; i < 7; i++)
348  {
349  G4RotationMatrix* rotFiber = new G4RotationMatrix;
350  rotFiber->rotateX(90 * degree);
351  rotFiber->rotateY(i * 25.72 * degree);
352  G4ThreeVector posFiber = G4ThreeVector(0, 152 * nanometer, 0);
353  posFiber.rotateZ(i * 25.72 * degree);
354  new G4PVPlacement(rotFiber,
355  posFiber,
356  logicEnv,
357  "physi env",
358  logicBoxros,
359  false,
360  0);
361 
362  rotFiber = new G4RotationMatrix;
363  rotFiber->rotateX(90 * degree);
364  rotFiber->rotateY((7 + i) * 25.72 * degree);
365  posFiber = G4ThreeVector(0, 152 * nanometer, 0);
366  posFiber.rotateZ((7 + i) * 25.72 * degree);
367  new G4PVPlacement(rotFiber,
368  posFiber,
369  logicEnv,
370  "physi env",
371  logicBoxros,
372  false,
373  0);
374 
375  rotFiber = new G4RotationMatrix;
376  rotFiber->rotateX(90 * degree);
377  rotFiber->rotateY((25.72 + (i - 14) * 51.43) * degree);
378  posFiber = G4ThreeVector(-36.5 * nanometer, 312 * nanometer, 0);
379  posFiber.rotateZ((i - 14) * 51.43 * degree);
380  new G4PVPlacement(rotFiber,
381  posFiber,
382  logicEnv,
383  "physi env",
384  logicBoxros,
385  false,
386  0);
387 
388  rotFiber = new G4RotationMatrix;
389  rotFiber->rotateX(90 * degree);
390  rotFiber->rotateY(180 * degree);
391  rotFiber->rotateY((i - 21) * 51.43 * degree);
392  posFiber = G4ThreeVector(-103 * nanometer, 297 * nanometer, 0);
393  posFiber.rotateZ((i - 21) * 51.43 * degree);
394  new G4PVPlacement(rotFiber,
395  posFiber,
396  logicEnv,
397  "physi env",
398  logicBoxros,
399  false,
400  0);
401 
402  }
403 
404  if (fBuildBases)
405  {
406  // Histones
407  G4Tubs* solidHistone = new G4Tubs("solid histone",
408  0,
409  3.25 * nanometer,
410  2.85 * nanometer,
411  0 * degree,
412  360 * degree);
413  G4LogicalVolume* logicHistone = new G4LogicalVolume(solidHistone,
414  waterMaterial,
415  "logic histone");
416 
417  //Base pair
418  G4Orb* solidBp1 = new G4Orb("blue sphere", 0.17 * nanometer);
419  G4LogicalVolume* logicBp1 = new G4LogicalVolume(solidBp1,
420  waterMaterial,
421  "logic blue sphere");
422  G4Orb* solidBp2 = new G4Orb("pink sphere", 0.17 * nanometer);
423  G4LogicalVolume* logicBp2 = new G4LogicalVolume(solidBp2,
424  waterMaterial,
425  "logic pink sphere");
426 
427  //Phosphodiester group
428 
429  G4Orb* solidSugar_48em1_nm = new G4Orb("sugar", 0.48 * nanometer);
430 
431  G4ThreeVector posi(0.180248 * nanometer,
432  0.32422 * nanometer,
433  0.00784 * nanometer);
434  G4UnionSolid* uniDNA = new G4UnionSolid("move",
435  solidSugar_48em1_nm,
436  solidSugar_48em1_nm,
437  0,
438  posi);
439 
440  G4ThreeVector posi2(-0.128248 * nanometer,
441  0.41227 * nanometer,
442  0.03584 * nanometer);
443  G4UnionSolid* uniDNA2 = new G4UnionSolid("move2",
444  solidSugar_48em1_nm,
445  solidSugar_48em1_nm,
446  0,
447  posi2);
448 
449  /************************************************************************
450  Phosphodiester group Position
451  ************************************************************************/
452 
453  for (G4int n = 2; n < 200; n++)
454  {
455  G4double SP1[2][3] = {
456  { (-0.6 * nanometer) * cos(n * 0.26),
457  0, (0.6* nanometer) * sin(n * 0.26) },
458  { (0.6 * nanometer) * cos(n * 0.26),
459  0, (-0.6 * nanometer) * sin(0.26 * n) }
460  };
461  G4double matriceSP1[3][3] = {
462  { cos(n * 0.076), -sin(n * 0.076), 0 },
463  { sin(n * 0.076), cos(n * 0.076), 0 },
464  { 0, 0, 1 }
465  };
466  G4double matriceSP2[2][3];
467 
468  for (G4int i = 0; i < 3; i++)
469  {
470  G4double sumSP1 = 0;
471  G4double sumSP2 = 0;
472  for (G4int j = 0; j < 3; j++)
473  {
474  sumSP1 += matriceSP1[i][j] * SP1[0][j];
475  sumSP2 += matriceSP1[i][j] * SP1[1][j];
476  }
477  matriceSP2[0][i] = sumSP1;
478  matriceSP2[1][i] = sumSP2;
479  }
480 
481  G4double heliceSP[3] = {
482  (4.85 * nanometer) * cos(n * 0.076),
483  (4.85 * nanometer) * sin(n * 0.076),
484  (n * 0.026 * nanometer)
485  };
486 
487  for (G4int i = 0; i < 3; i++)
488  {
489  matriceSP2[0][i] += heliceSP[i];
490  matriceSP2[1][i] += heliceSP[i];
491  }
492  G4ThreeVector posSugar1(matriceSP2[0][2],
493  matriceSP2[0][1],
494  (matriceSP2[0][0]) - (4.25 * nanometer));
495  G4ThreeVector posSugar2(matriceSP2[1][2],
496  matriceSP2[1][1],
497  (matriceSP2[1][0]) - (5.45 * nanometer));
498 
499  ostringstream ss;
500  ss << "sugar_" << n;
501  name = ss.str().c_str();
502  ss.str("");
503  ss.clear();
504 
505  // snprintf(name, countof(name), "sugar %d", n);
506  uniDNA = new G4UnionSolid(name,
507  uniDNA,
508  solidSugar_48em1_nm,
509  0,
510  posSugar1);
511 
512  ss << "sugar_" << n;
513  name = ss.str().c_str();
514  ss.str("");
515  ss.clear();
516 
517  // snprintf(name, countof(name), "sugar %d", n);
518  uniDNA2 = new G4UnionSolid(name,
519  uniDNA2,
520  solidSugar_48em1_nm,
521  0,
522  posSugar2);
523  }
524  G4LogicalVolume* logicSphere3 = new G4LogicalVolume(uniDNA,
525  waterMaterial,
526  "logic sugar 2");
527  G4LogicalVolume* logicSphere4 = new G4LogicalVolume(uniDNA2,
528  waterMaterial,
529  "logic sugar 4");
530 
531  /**************************************************************************
532  Base pair Position
533  **************************************************************************/
534  for (G4int n = 0; n < 200; n++)
535  {
536  G4double bp1[2][3] = {
537  { (-0.34 * nanometer) * cos(n * 0.26),
538  0, (0.34* nanometer) * sin(n * 0.26) },
539  { (0.34 * nanometer) * cos(n * 0.26),
540  0, (-0.34 * nanometer) * sin(0.26 * n) }
541  };
542  G4double matriceBP1[3][3] = {
543  { cos(n * 0.076), -sin(n * 0.076), 0 },
544  {sin(n * 0.076), cos(n * 0.076), 0 },
545  { 0, 0, 1 }
546  };
547  G4double matriceBP2[2][3];
548 
549  for (G4int i = 0; i < 3; i++)
550  {
551  G4double sumBP1 = 0;
552  G4double sumBP2 = 0;
553  for (G4int j = 0; j < 3; j++)
554  {
555  sumBP1 += matriceBP1[i][j] * bp1[0][j];
556  sumBP2 += matriceBP1[i][j] * bp1[1][j];
557  }
558  matriceBP2[0][i] = sumBP1;
559  matriceBP2[1][i] = sumBP2;
560  }
561  G4double heliceBP[3] = {
562  (4.8 * nanometer) * cos(n * 0.076),
563  (4.8 * nanometer) * sin(n * 0.076),
564  n * 0.026 * nanometer
565  };
566 
567  for (G4int i = 0; i < 3; i++)
568  {
569  matriceBP2[0][i] += heliceBP[i];
570  matriceBP2[1][i] += heliceBP[i];
571  }
572  G4ThreeVector position1(matriceBP2[0][2],
573  matriceBP2[0][1],
574  matriceBP2[0][0] - (4.25 * nanometer));
575  G4ThreeVector position2(matriceBP2[1][2],
576  matriceBP2[1][1],
577  matriceBP2[1][0] - (5.45 * nanometer));
578 
579  new G4PVPlacement(0,
580  position1,
581  logicBp1,
582  "physi blue sphere",
583  logicSphere3,
584  false,
585  0);
586  new G4PVPlacement(0,
587  position2,
588  logicBp2,
589  "physi pink sphere",
590  logicSphere4,
591  false,
592  0);
593  }
594 
595  /****************************************************************************/
596  // Initial position of different elements
597  /****************************************************************************/
598  // DNA and histone positions
599  for (int j = 0; j < 90; j++)
600  {
601  // DNA (bp-SP)
602  G4RotationMatrix* rotStrand1 = new G4RotationMatrix;
603  rotStrand1->rotateZ(j * -51.43 * degree);
604  G4ThreeVector posStrand1(-2.7 * nanometer,
605  9.35 * nanometer,
606  (-69.9 * nanometer) + (j * 1.67 * nanometer));
607  posStrand1.rotateZ(j * 51.43 * degree);
608  new G4PVPlacement(rotStrand1,
609  posStrand1,
610  logicSphere3,
611  "physi sugar 2",
612  logicEnv,
613  false,
614  0);
615 
616  G4RotationMatrix* rotStrand2 = new G4RotationMatrix;
617  rotStrand2->rotateZ(j * -51.43 * degree);
618  G4ThreeVector posStrand2(-2.7 * nanometer,
619  9.35 * nanometer,
620  (-68.7 * nanometer) + (j * 1.67 * nanometer));
621  posStrand2.rotateZ(j * 51.43 * degree);
622  new G4PVPlacement(rotStrand2,
623  posStrand2,
624  logicSphere4,
625  "physi sugar 4",
626  logicEnv,
627  false,
628  0);
629 
630  // histones
631  G4RotationMatrix* rotHistone = new G4RotationMatrix;
632  rotHistone->rotateY(90 * degree);
633  rotHistone->rotateX(j * (-51.43 * degree));
634  G4ThreeVector posHistone(0.0,
635  9.35 * nanometer,
636  (-74.15 + j * 1.67) * nanometer);
637  posHistone.rotateZ(j * 51.43 * degree);
638  new G4PVPlacement(rotHistone,
639  posHistone,
640  logicHistone,
641  "PV histone",
642  logicEnv,
643  false,
644  0);
645  }
646  /************************************************************************/
647  // Visualisation colors
648  /************************************************************************/
649 
650  logicBp1->SetVisAttributes(&visInvCyan);
651  logicBp2->SetVisAttributes(&visInvPink);
652 
653  logicSphere3->SetVisAttributes(&visInvWhite);
654  logicSphere4->SetVisAttributes(&visInvRed);
655 
656  logicHistone->SetVisAttributes(&visInvBlue);
657  }
658  }
659 
660  G4cout << "Geometry has been loaded" << G4endl;
661  return physiWorld;
662 }