#Rasmol-script
#load pdb H:\publick_html\t3_files\rna-1h4s.pdb
load pdb rna-1h4s.pdb
reset
slab off
rotate z -172
rotate y 1
rotate x 83
restrict none
select all
strands

echo -------
echo This is a Rasmol script to demonstrate tRNA structure 1H4S
echo To continue, press Space
echo -------
pause
echo
reset
slab off
rotate z 0
rotate y 7
rotate x -114

select all
strands off
wireframe 50
define helix1 4-7T or 66-69T
echo | helix GGAG CCUC (4-7 69-66) is defined as "helix1"
define helix2 10-13T or 22-25T
echo | helix GCGC CGCG (10-13 25-22) is defined as "helix2"
define helix3 26-32T or 38-44T
echo | helix ACCUCGU GGGAGCA (26-32 44-38) is defined as "helix3"
define helix4 49-53T or 61-65T
echo | helix GCUGG UGACC (49-53 65-61) is defined as "helix4"
#pause
define helixes helix1,helix2,helix3,helix4
echo 
echo | "helixes" is for joint of helix1, helix2, helix3, helix4
pause
echo _______ 

#define bungle1 9T
#define bungle2 45T
#echo bungles A (9), G (45),
#define loop1 16-17T or 20-21T
#define loop2 33-37T
#echo loops CCC UA (16-17 20-21), UCGGG (33-37)

define loop1 8-9T
define loop2 14-21T
define loop3 33-37T
define loop4 45-48T
define loop5 54-60T
echo | loop UA (8-9) is defined as loop1
echo | loop AGCCCGGUA (14-21) is defined as loop2
echo | loop UCGGG (33-37) is defined as loop3
echo | loop GGGC (45-48) is defined as loop4
echo | loop 5MU PSU CAGAU(54-60) is defined as loop5
define loops loop1 or loop2 or loop3 or loop4 or loop5
echo
echo | "loops" is for joint of loop1, loop2, loop3, loop4, loop5
pause
echo _______ 

define knot1 9T or 23T
define knot2 10T or 45T
define knot3 18T or 55T
define knot4 22T or 46T
define knot5 26T or 44T
define knot6 49T or 65T
define knot7 54T or 58T
echo | apocryphal pairs AC (9 23), GG (10 45), G PSU (18 55),
echo GG (22 46), AG (26 44), GU (49 65), 5MU G (54 58)
echo is defined as knot1, knot2, knot3, knot4, knot5, knot6, knot7
define knots knot1 or knot2 or knot3 or knot4 or knot5 or knot6 or knot7
echo | "knots" is for joint of knot1, knot2, knot3, knot4, knot5, knot6, knot7
pause
echo _______ 

#define pair1 8T or 14T
#define pair2 15T or 48T
#define pair3 18T or 55T
#define pair4 19T or 56T
#define pair5 22T or 46T
#define pair6 58T or 54T

define IIIlend 4T
define Vlend 69T
define lends 4T or 69T
echo | 5' lend is defined as "Vlend"
echo | 3' lend is defined as "IIIlend"
echo | "lends" is both of 3' and 5' lends 
echo _______ 
pause

#define anticodon_loop 33-37T
define anticodon 34T or 35T or 36T
echo | the CGG 'anticodon' (34,35,36) is defined
echo _______ 
echo press Space to continue
pause
 

restrict none
select all
backbone 100
pause
select helix1
wireframe 50
colour purple
pause
select helix2
wireframe 50
colour yellow
pause
select helix3
wireframe 50
colour green
pause
select helix4
wireframe 50
colour orange
pause
select knots
wireframe 50
colour blue
pause
select U8T or A14T or  A9T or G15T or C48T or G19T or C56T
wireframe 50
colour white
pause
select loop1 or loop4
wireframe 50
pause
select loop2 or loop5
wireframe 50
pause
select loop3
wireframe 50
pause
select anticodon
colour red
wireframe 100
pause
select all
wireframe 50
backbone off
select anticodon
wireframe 100
select all
echo 
echo --------
echo GOOD LUCK!!!
echo --------