Александр Юрьевич, а можно восстановить тему пикотехнология биомолекул, начиная с предпоследнего стирания уродами (с Нового года).  Вы же вроде как копировали.

Кушелев: У меня есть копия 5 страниц темы: Скрипт-генератор ДНК / РНК (86 сообщений).

Предпоследнее сообщение от 25.04.2011 09:31:42

Практически все сообщения из темы "Пикотехнология биомолекул" я копировал в тему "Формы, механизмы, энергия наномира", но саму тему "Пикотех" я не копировал.

Так что копии важных сообщений можно взять отсюда: http://nanoworld88.narod.ru/forum/index.htm

Но 28-ая часть пока без картинок. Картинки весят 0.5 Gb, поэтому через GPRS загрузить их на Яндекс нереально. Могу привезти их на DVD в Москву и передать Ярославу, чтобы он залил на Яндекс.

Кушелев: Нашёл в архиве с 18 по 23 страницы темы "Пространственная структура биомолекул"

Мне удалось смоделировать псевдоуридиловую петлю без "выкручивания суставов", т.е. используя углы поворотов, кратные 120 градусам:

http://fotki.yandex.ru/users/sokolik1867/view/375386/

Скрипт:

aa = #(); ax = #(); ay = #(); nuclcol = #()
-- adenosine, cytosine, guanine, timidine, uracil, inosine, pseudouracil, dihydrouracil, methyl inosine, x-circles maximum, w-methyl-2-guanine, v-methyl-1-guanine
nucl = #("a","c","g","t","u","i","p","d","m","x","w","v")
nuclcolor = #([300,0,0],[200,200,0],[100,0,200],[0,80,50],[0,0,255],[200,0,200],[300,150,0],[0,200,0],[0,200,200],[255,255,255],[100,100,100])

Я думаю, что возможны и другие композиции углов. В данном случае продемонстрирована сама возможность такого моделирования.
--*****************************************************************************************************************
seq = #("a","c","c","a","c","c","u","g","c","u","c","a","g","g","c","c","u","u","c","g","a","p","t")
--*****************************************************************************************************************
-- complement
complement = #("0","0","0","0","g","g","g","c","g","u","g","u","c","c","g","g","0","0","0","0","0","0","0")
ci = #(         0 , 0 , 0 , 0 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 0 , 0 , 0 , 0 , 0 , 0 , 0 )     

--*****************************************************************************************************************
--                                                      turn
anglecomp1 = #(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,120,240,120,0)
anglecomp2 = #(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,120,0,120,0,0)
--*****************************************************************************************************************
trnk = torus radius1:0.1 radius2:0.04 segs:3 sides:3 position: [0,0,0] wirecolor:[200,200,200]
Converttomesh trnk

newmat = multimaterial name:"MyMultiMat" numsubs: (13)
newmat[1].faceted = on
newmat[2].faceted = on
newmat[3].faceted = on
newmat[4].faceted = on
newmat[5].faceted = on
newmat[6].faceted = on
newmat[7].faceted = on
newmat[8].faceted = on
newmat[9].faceted = on
newmat[10].faceted = on
newmat[11].faceted = on
newmat[12].faceted = on
newmat[13].faceted = on
newmat[1].diffuse = (color 300 0 0)
newmat[2].diffuse = (color 200 200 0)
newmat[3].diffuse = (color 100 0 200)
newmat[4].diffuse = (color 0 80 50)
newmat[5].diffuse = (color 0 0 255)
newmat[6].diffuse = (color 200 0 200)
newmat[7].diffuse = (color 300 150 0)
newmat[8].diffuse = (color 0 200 0)
newmat[9].diffuse = (color 0 200 200)
newmat[10].diffuse = (color 100 100 100)
newmat[11].diffuse = (color 100 100 100)
newmat[12].diffuse = (color 255 255 255)
newmat[13].diffuse = (color 0 0 0)
--
m3 = mesh vertices: #([-2.828,-45.5,-2.828]
,[2.828,-45.5,-2.828],[2.828,-45.5,2.828],[-2.828,-45.5,2.828],[-2.828,-61.5,-2.828],[2.828,-61.5,-2.828]
,[2.828,-61.5,2.828],[-2.828,-61.5,2.828],[-2.828,-53.5,-8.485],[-5.657,-49.5,-5.657],[-8.485,-53.5,-2.828]
,[-5.657,-57.5,-5.657],[8.485,-53.5,2.828],[5.657,-49.5,5.657],[2.828,-53.5,8.485],[5.657,-57.5,5.657]
,[5.657,-49.5,-5.657],[2.828,-53.5,-8.485],[5.657,-57.5,-5.657],[8.485,-53.5,-2.828],[-5.657,-49.5,5.657]
,[-8.485,-53.5,2.828],[-5.657,-57.5,5.657],[-2.828,-53.5,8.485]) \
faces: #([1,3,2],[1,4,3],[5,6,7],[5,7,8],[9,11,10],[9,12,11],[13,14,15],[13,15,16],[17,19,18],[17,20,19],[21,22,23],[21,23,24]
,[1,2,17],[17,18,9],[9,10,1],[1,17,9],[10,22,4],[4,1,10],[10,11,22],[22,21,4],[11,5,23],[23,22,11],[11,12,5],[5,8,23]
,[12,18,6],[6,5,12],[12,9,18],[18,19,6],[8,16,24],[24,23,8],[16,15,24],[8,7,16],[15,3,21],[21,24,15],[15,14,3]
,[3,4,21],[14,20,2],[2,3,14],[14,13,20],[20,17,2],[13,7,19],[19,20,13],[13,16,7],[7,6,19]) \

m3.material = newmat[12]
m4 = copy m3
m4.material = newmat[12]
m4.pivot = [0,-40,0]
rotate m4 -120 [0,0,1]
move m4 [-7.5,-0.5,0]
m6 = copy m3 
m6.material = newmat[12]
m13 = copy m3
m13.material = newmat[12]
m13.pivot = [0,-66,0]
rotate m13 -72 [1,0,0]
m14 = copy m13
m14.material = newmat[12]
g1 = group #(m6, m14)
g1.pivot = [0,-40,0]
rotate g1 -45 [0,0,1]
move g1 [-5.5,2.5,0]
ungroup g1
m5 = copy m6
m5.material = newmat[12]
m7 = copy m4
m7.material = newmat[12]
g2 = group #(m5, m7)
g2.pivot = [0,-40,0]
rotate g2 180 [0,1,0]
ungroup g2
m8 = mesh vertices: #([-4,0,-8],[0,-4,-8],[4,0,-8],[0,4,-8],[-4,0,8],[0,-4,8],[4,0,8],[0,4,8]
,[-8,-4,0],[-8,0,-4],[-8,4,0],[-8,0,4],[8,-4,0],[8,0,-4],[8,4,0],[8,0,4]
,[0,-8,-4],[-4,-8,0],[0,-8,4],[4,-8,0],[0,8,-4],[-4,8,0],[0,8,4],[4,8,0]) \
faces: #([1,3,2],[1,4,3],[5,6,7],[5,7,8],[9,11,10],[9,12,11],[13,14,15],[13,15,16],[17,19,18],[17,20,19],[21,22,23],[21,23,24]
,[1,2,17],[17,18,9],[9,10,1],[1,17,9],[10,22,4],[4,1,10],[10,11,22],[22,21,4],[11,5,23],[23,22,11],[11,12,5],[5,8,23]
,[12,18,6],[6,5,12],[12,9,18],[18,19,6],[8,16,24],[24,23,8],[16,15,24],[8,7,16],[15,3,21],[21,24,15],[15,14,3]
,[3,4,21],[14,20,2],[2,3,14],[14,13,20],[20,17,2],[13,7,19],[19,20,13],[13,16,7],[7,6,19]) \

m8.material = newmat[11]
rotate m8 45 [1,0,0]
rotate m8 90 [0,0,1]
move m8 [-37.5,0,0]
m9 = copy m8
m9.material = newmat[11]
m9.pivot = [-37.5,-13,-0.5]
rotate m9 72 [1,0,0]
m10 = copy m8
m10.material = newmat[11]
m10.pivot = [-37.5,-13,-0.5]
rotate m10 144 [1,0,0]
m11 = copy m8
m11.material = newmat[11]
m11.pivot = [-37.5,-13,-0.5]
rotate m11 18 [1,0,0]
rotate m11 90 [0,0,1]
rotate m11 180 [1,0,0]
rotate m11 -18 [1,0,0]
move m11 [0,7,24]
m12 = copy m9
m12.material = newmat[12]
m12.pivot = [-37.5,-23.5,15]
rotate m12 -120 [0,0,1]
attach m3 m4
attach m5 m7
attach m6 m13
attach m3 m5
attach m3 m6
attach m8 m9
attach m8 m11
attach m3 m10
attach m12 m14
attach m3 m12
--
for k = 14 to 23 do(
-- adenosine, cytosine, guanine, timidine, uracil, inosine, pseudouracil, dihydrouracil, methyl inosine, x-circles maximum, w-methyl-2-guanine, v-methyl-1-guanine
if (seq[k] == nucl[10]) then (ai = #(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1); axi = #(1,1,1,1,1,1,1,1); ayi = #(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1); nuclcol = nuclcolor[10]; nc=10)
if (seq[k] == nucl[1]) then (ai = #(0,0,0,1,1,1,1,1,1,1,1,1,0,0,1); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,0,0,1,0,1,0,1,0); nuclcol = nuclcolor[1]; nc=1)
if (seq[k] == nucl[2]) then (ai = #(0,0,0,1,1,1,1,1,1,1,0,1,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[2]; nc=2)
if (seq[k] == nucl[3]) then (ai = #(0,1,0,1,1,1,1,1,1,1,1,1,0,1,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,0,0,0,0,0,0,0,0,1,0,1,0,1,0); nuclcol = nuclcolor[3]; nc=3)
if (seq[k] == nucl[4]) then (ai = #(0,1,0,1,1,1,1,1,1,1,1,0,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[4]; nc=4)
if (seq[k] == nucl[5]) then (ai = #(0,0,0,1,1,1,1,1,1,1,1,0,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[5]; nc=5)
if (seq[k] == nucl[6]) then (ai = #(0,0,0,1,1,1,1,1,1,1,1,1,1,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,0,0,1,0,1,0,1,0); nuclcol = nuclcolor[6]; nc=6)
if (seq[k] == nucl[7]) then (ai = #(0,0,0,1,1,1,1,1,1,0,1,1,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[7]; nc=7)
if (seq[k] == nucl[8]) then (ai = #(0,0,0,1,1,1,1,1,1,1,0,1,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[8]; nc=8)
if (seq[k] == nucl[9]) then (ai = #(0,0,0,1,1,1,1,1,1,1,1,1,0,1,1); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,0,0,1,0,1,0,1,0); nuclcol = nuclcolor[9]; nc=9)
--
element1 = box length:1 width:1 height:1  position:[0,0,-0.5] wirecolor: nuclcol
Converttomesh element1
for i = 1 to 3 do for j = 1 to 5 do (n = i + 3*(j-1)
if ai[n] > 0 then (aa[n] = box length:10 width:10 height:10 position:[10*(i-2),10*(j-5),10*0.5-10] wirecolor: nuclcol
select #(aa[n]); macros.run  "Modifier stack" "convert_to_Mesh"
attach element1 aa[n]
element1.material = newmat[nc]))
element2 = copy m8
element3 = copy m3
attach element1 element3
--
if ci[k] > 0 then (
--
if (complement[k] == nucl[10]) then (ai = #(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1); axi = #(1,1,1,1,1,1,1,1); ayi = #(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1); nuclcol = nuclcolor[10]; nc=10)
if (complement[k] == nucl[1]) then (ai = #(0,0,0,1,1,1,1,1,1,1,1,1,0,0,1); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,0,0,1,0,1,0,1,0); nuclcol = nuclcolor[1]; nc=1)
if (complement[k] == nucl[2]) then (ai = #(0,0,0,1,1,1,1,1,1,1,0,1,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[2]; nc=2)
if (complement[k] == nucl[3]) then (ai = #(0,1,0,1,1,1,1,1,1,1,1,1,0,1,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,0,0,0,0,0,0,0,0,1,0,1,0,1,0); nuclcol = nuclcolor[3]; nc=3)
if (complement[k] == nucl[4]) then (ai = #(0,1,0,1,1,1,1,1,1,1,1,0,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[4]; nc=4)
if (complement[k] == nucl[5]) then (ai = #(0,0,0,1,1,1,1,1,1,1,1,0,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[5]; nc=5)
if (complement[k] == nucl[6]) then (ai = #(0,0,0,1,1,1,1,1,1,1,1,1,1,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,0,0,1,0,1,0,1,0); nuclcol = nuclcolor[6]; nc=6)
if (complement[k] == nucl[7]) then (ai = #(0,0,0,1,1,1,1,1,1,0,1,1,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[7]; nc=7)
if (complement[k] == nucl[8]) then (ai = #(0,0,0,1,1,1,1,1,1,1,0,1,0,0,0); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,1,0,1,0,1,0,0,0); nuclcol = nuclcolor[8]; nc=8)
if (complement[k] == nucl[9]) then (ai = #(0,0,0,1,1,1,1,1,1,1,1,1,0,1,1); axi = #(0,0,1,1,0,0,0,0); ayi = #(0,1,0,0,0,0,0,0,0,1,0,1,0,1,0); nuclcol = nuclcolor[9]; nc=9)
element4 = box length:1 width:1 height:1  position:[0,0,-0.5] wirecolor: nuclcol
Converttomesh element4
for i = 1 to 3 do for j = 1 to 5 do (n = i + 3*(j-1)
if ai[n] > 0 then (aa[n] = box length:10 width:10 height:10 position:[10*(i-2),10*(j-5),10*0.5-10] wirecolor: nuclcol
select #(aa[n]); macros.run  "Modifier stack" "convert_to_Mesh"
attach element4 aa[n]
element4.material = newmat[nc]))
element5 = copy m8
element6 = copy m3
attach element4 element6
attach element4 element5
element4.pivot = [0,0,0]
if ci[k] == 1 then (rotate element4 180 [1,0,0])
-- if ci[k] == 2 then (rotate element4 180 [1,0,0]; rotate element4 90 [0,1,0]; move element4 [0,0,0])
if ci[k] == 3 then (rotate element4 180 [1,0,0]; rotate element4 180 [0,1,0])
attach element1 element4
)
-- first vector
gr1 = group #(element1,trnk)
gr1.pivot = [-37.451, -2.887, 14.138]
rotate gr1 anglecomp1[k] [0, -27.384, -9.84]
if k == 40 then (rotate gr1 -90 [0, 0, 1] ; rotate gr1 -20 [0, 1, 0] )
ungroup gr1
-- second vector
gr2 = #(element1, element2, trnk)
gr2.pivot = [-43.391, -10.855, 7.631]
rotate gr2 anglecomp2[k] [-11.880, -2.245, -8.094]
ungroup gr2
-- translation vector
attach trnk element1
attach trnk element2
move trnk [0,-50, 0]
trnk.pivot = [-60,0,0]
-- translation angles
rotate trnk 36 [0, 1, 0]
-- rotate trnk 35 [0, 0, 1]
)
--
delete m3
delete m8
trnk.rotation.controller[2].controller.value = 0
-- animate on
-- at time 100 trnk.rotation.controller[2].controller.value = 360

Вы неверно прочитали: я предложила модель ПСЕВДОУРАЦИЛОВОЙ петли, а Вы мне об антикодоновой... Кстати метилинозин не принадлежит антикодоновому триплету тРНК, даже если Вы обнаружили это в своём модельном эксперименте.
Кроме этого, Вы моделируете вращение всей тРНК с "обрезанием" кодонов иРНК, а я моделирую 3 изоакцепторные модели тРНК, в структуре которых поворот уже реализован и выбор в рибосоме происходит по первому нуклеотиду антикодонов этих изоакцепторных вариантов тРНК.