// PoVRay 3.5 Scene File " helix.pov" // created by Dr Engelbert Buxbaum // date 30.04.2004 // Amphipatic alpha-helix, N-terminal mitochondrial import sequence // MLSLRQSIRFFKPATRTL in COX4_Yeast (Cyt c oxidase subunit 4 precursor) // Accession No P04037 //-------------------------------------------------------------------------- #version 3.5; global_settings { assumed_gamma 1 } //------------------------ Surface properties of ribbon ----------------------- #declare RIBBON_FINISH = finish { ambient 0.2 diffuse 0.6 phong 0.5 phong_size 5 } // -------------------- Standard Group colours for amino acids ---------------- #declare Positive_Colour = rgb< 20, 90, 255 >; // K, R, H #declare Negative_Colour = rgb< 230, 10, 10 >; // D, E #declare Polar_Colour = rgb< 250, 150, 0 >; // S, T #declare Hydrophob_Colour = rgb< 15, 130, 15 >; // A, V, I, L #declare Aromatic_Colour = rgb< 101, 86, 47 >; // F, Y, W #declare Sulphur_Colour = rgb< 230, 230, 0 >; // C, M #declare Amin_Colour = rgb< 0, 220, 220 >; // N, Q #declare Structure_Colour = rgb< 220, 150, 130 >; // G, P // ---------------------------------- camera ---------------------------------- #declare Winkel = 110; #declare Camera0 = camera { angle Winkel // front view location <0.0 , 0.0 ,-10.0> right x*image_width/image_height look_at <0.0 , 0.0 , 0.0>} #declare Camera1 = camera { angle Winkel // diagonal view location <5.0 , 2.5 ,-4.0> right x*image_width/image_height look_at <0.0 , 0.0 , 0.0>} #declare Camera2 = camera { angle Winkel // right side view location <10.0 , 0.0 , 0.0> right x*image_width/image_height look_at <0.0 , 0.0 , 0.0>} #declare Camera3 = camera {angle Winkel // top view location <0.0 , 30.0 ,-0.01> right x*image_width/image_height look_at <0.0 , 0.0 , 0.0>} camera{Camera0} // select camera // --------------------------------- light ------------------------------------ light_source { <-20, 20, -20> // from top left color rgb< 255, 255, 255> // pure white /* fade_distance 5 fade_power 1 area_light <5, 0, 0>, <0, 0, 5>, 5, 5 adaptive 1 jitter */ } // --------------------------------------- rod -------------------------------- #declare P_R = 0.10; #declare P_H = 0.40; #declare Profile = union { sphere { <0, P_H>, P_R } cylinder { <0, -P_H, 0 >, <0, P_H, 0 >, P_R } sphere { <0, -P_H, 0 >, P_R } finish { RIBBON_FINISH } translate < 0, -7, 0 > // y-translation to center helix } // ------------------------- many rods joined to form helix ---------------------- #declare Grad = 100; // 3.6 amino acids per turn in alpha helix = 100 degrees #declare Radius_Major = 2.00; // outer diameter of helix #declare N = 100; // minimum about 30 for smooth tape #declare Turn_Height = 2.0; // how far the turns are streched appart from each other #declare Nr = 0; // loop variable #declare Factor = Turn_Height * P_H / N; // calculate only once #declare Factor2 = Grad / N; #while (Nr < N) // M = Methionine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Sulphur_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 2*N) // L = Leucine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Hydrophob_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 3*N) // S = Serine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Polar_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 4*N) // L = Leucine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Hydrophob_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 5*N) // R = Arginine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Positive_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 6*N) // Q = Glutamine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Amin_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 7*N) // S = Serine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Polar_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 8*N) // I = Isoleucine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Hydrophob_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 9*N) // R = Arginine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Positive_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 10*N) // F = Phenylalanine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Aromatic_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 11*N) // F = Phenylalanine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Aromatic_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 12*N) // K = Lysine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Positive_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 13*N) // P = Proline object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Structure_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 14*N) // Ala object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Hydrophob_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 15*N) // T = Threonine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Polar_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 16*N) // R = Arginine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Positive_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 17*N) // T = Threonine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Polar_Colour } } #declare Nr = Nr + 1; #end #while (Nr < 18*N) // L = Leucine object { Profile translate < Radius_Major, Nr*Factor, 0 > rotate < 0, Nr*Factor2, 0 > pigment { Aromatic_Colour } } #declare Nr = Nr + 1; #end