load H:\Term3\CreditWorks\Credit1\1eiy.pdb
define helix1 rna and (1-7,66-72)
echo helix1 is p-type stem
define helix2 rna and (10-13,22-25)
echo helix2 is D-stem
define helix3 rna and (26-31,39-44)
echo helix2 is anticodon stem
define helix4 rna and (49-53,61- 65)
echo helix4 is T-stem
define helixes rna and (1-7,66-72,10-13,22-25,26-31,39-44,49-53,61-65)
echo helixes are four stems that form the clover leaf
define loop1 rna and (14-21)
echo loop1 is D-loop
define loop2 rna and (32-38)
echo loop2 is anticodon loop
define loop3 rna and (54-60)
echo loop3 is T-loop
define loop4 rna and (7-10,25,26,65,66)
echo loop4 is multiloop
define loop5 rna and (44-48)
echo loop5 is V-loop
define loops rna and (14-21,32-38,54-60,7-10,25,26,65,6644-48)
echo These are five loops found in tRNA secondary structure
define knot1 rna and (8,14)
echo knot1 is contact between anticodon stem and V-loop
define knot2 rna and (15,48)
echo knot2 is contact between D-loop and V-loop
define knot3 rna and (16,59)
echo knot3 is contact between D-loop and T-loop
define knot4 rna and (18,55)
echo knot4 is contact between D-loop Tnd T-loop
define knot5 rna and (19,56)
echo knot5 is contact between D-loop Tnd T-loop
define knot6 rna and (45,9)
echo knot6 is contact between D-helix and V-loop
define knots rna and (8,14,15,48,16,59,18,55,45,9)
echo knots are contacts that conform the 3D-structure of tRNA
define lands rna and (73-76)
echo this is 3`-end
define anticodon rna and (34-36) 
echo This is Anticodon
script 1eiy.def
echo this a complex between tRNA and protein
pause
restrict rna
zoom 270
center selected
echo this is tRNA
pause
wireframe 20
select helix1
wireframe 50
color yellow
echo this is p-type stem
pause
select helix1
wireframe 20
select helix2
wireframe 50
color green
echo this is D-stem
pause
select helix2
wireframe 20
select helix3
wireframe 50
color purple
echo this is anticodon stem
pause
select helix3
wireframe 20
select helix4
wireframe 50
color cyan
echo this is T-stem
pause
select helix5
wireframe 20
select loop1
wireframe 50
color grey
echo this is D-loop
pause
select loop1
wireframe 20
select loop2
wireframe 50
color orange
echo this is anticodon loop
pause
select loop2
wireframe 20
select loop3
wireframe 50
color violet
echo this is T-loop
pause
select loop3
wireframe 20
select loop4
wireframe 50
color pink
echo this is multiloop
pause
select loop4
wireframe 20
select loop5
wireframe 50
color yellow
echo this is V-loop
pause
select loop5
wireframe 20
select helixes
wireframe 50
echo these are complementary-based sites in the molecule
pause
select helixes
wireframe 20
select loops
wireframe 50
echo and these are loops
pause
select loops
wireframe 20
select knot1
wireframe 70
echo These nucleotids bind
pause
select helix1
wireframe 50
echo anticodon stem
pause
select loop5
wireframe 50
echo and D-loop
pause
select rna
wireframe 20
select knot2
wireframe 70
echo These nucleotids bind
pause
select loop1
wireframe 50
echo D-lopp
pause
select loop5
wireframe 50
echo and V-loop
pause
select rna
wireframe 20
select knot3
wireframe 70
echo These nucleotids bind
pause
select loop1
wireframe 50
echo D-loop
pause
select loop3
wireframe 50
echo and T-loop
pause
select rna
wireframe 20
select knot4
wireframe 70
echo These nucleotids bind
pause
select loop1
wireframe 50
echo D-loop
pause
select loop3
wireframe 50
echo and T-loop
pause
select rna
wireframe 20
select knot5
wireframe 70
echo These nucleotids bind
pause
select loop1
wireframe 50
echo D-loop
pause
select loop3
wireframe 50
echo and T-loop
pause
select rna
wireframe 20
select knots
wireframe 70
echo and these are the five imortant pairs
pause
select rna
wireframe 40
echo This is tRNA
pause
select lands
wireframe 70 
echo this is 3`-end
pause
select anticodon
color red
wireframe 70
echo and this is GAA - anticodon
pause
select rna
wireframe 20
color grey
zoom 250
rotate x -60
echo now  we`re going to find stacking
pause
select rna and not (backbone,helixes)
wireframe 40
color green
echo These are locuses with possibility of stacking
pause
select rna and not (backbone,helixes)
color grey
select rna and (32-38) and not backbone
zoom 300
center selected
color red
wireframe 60
echo This is the first area of stacking
pause
select rna and (21,46,49,14,15,48)
center selected
color red
wireframe 60
echo This is the second area of stacking
pause
select rna and (54-58)
center selected
color red
wireframe 60
echo This is the third area of stacking
pause
echo and that`s all. Enloy life!