# This is a Rasmol script to demonstrate tRNA structure 1euy.
# In order to automatically load PDB file you may insert the following line
# load 1EUY.pdb      
# Be careful with directories and paths!
define   helix1   903-907b, 966-971b
define   helix2   910-913b, 922-925b
define   helix3   926-933b, 937-944b
define   helix4   949-953b, 961-965b
define helixes  helix1, helix2, helix3, helix4
echo tRNA helixes are defined as helix1, helix2, helix3, helix4   
#This text will be typed in command line
echo "helices" is for joint of helix1, helix2, helix3, helix4  
define loop1  914-921b
echo loop1 are defined as D-loop
#This text will be typed in command line 
define loop2  934-936b
echo loop2 are defined as anticodon loop
#This text will be typed in command line
define loop3  945-948b 
echo loop3 are defined as variable loop
#This text will be typed in command line
define loop4  954-960b
echo loop4 are defined as T-loop
#This text will be typed in command line
define loop5  908-910b, 925-926b, 944b, 949b, 965b 
echo loop5 are defined as main loop
#This text will be typed in command line
define knot1  913b, 922b
echo knot1 are defined as non-canonical pair A-A 
#This text will be typed in command line
define knot2  926b, 944b
echo knot2 are defined as non-canonical pair A-C
#This text will be typed in command line
define knot3  932b, 938b
echo knot3 are defined as non-canonical pair U-U
#This text will be typed in command line
define anticodon 934-936b
echo anticodon is CUG 
#This text will be typed in command line
define lends 902b, 976b
echo lends are 5'- and 3'-lends 
#This text will be typed in command line  
restrict rna 
wireframe 80
echo press any button to color 5'- and 3'-lends yellow  
pause
select lends
color yellow
echo press any button to color helix1 red
pause
select helix1
color red
echo press any button to color helix2 blue
pause
select helix2
color blue
echo press any button to color helix3 yellow
pause
select helix3
color yellow
echo press any button to color helix4 orange
pause
select helix4
color orange
echo press 
echo Enjoy stems of the best in the world tRNA!!!
pause        
# This command forces Rasmol to stop and wait for Enter
select knot1
color green
select knot2
color green
select knot3
color green
echo Non-canonical pairs are in green!!!
select anticodon
color purple
echo  CUG anticodon is in purple!!!
pause
echo Ciao!

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© Армаш Татьяна,2005