# This is a Rasmol script to demonstrate TYR-tRNA structure 1j1u.
# In order to automatically load PDB file you may insert the following line
# load 1j1u.pdb      
# Be careful with directories and paths!
#
# You may include all definitions in a separate file 1j1u.def and in this script
# just add a line
 script 1j1u.def
#

echo tRNA helixes are defined as helix1,helix2,helix3, helix4

   
#This text will be typed in command line

echo "helixes" is for joint of helix1,helix2,helix3, helix4 

restrict rna 
backbone 80 
wireframe off
select helix1
color purple
select helix2
color blue
select helix3
color yellow
select helix4
color orange
select helixes
wireframe 20  

select not helixes
color grey

echo helix 1 - for acceptor stem;
echo helix 2 - for D-stem;
echo helix 3 - for anticodon stem;
echo helix 4 - for T-stem;

echo Enjoy stems of tRNA!!!

pause

echo loop1 - for D-loop;
echo loop2 - for anticodon loop;
echo loop3 - for variable loop;
echo loop4 - for T-loop;

pause

echo non-Watson-Crick base-pairs are defined as knots     
  
select knots
color green
echo non-Watson-Crick base-pairs are define as knots 
echo Non-canonical pairs are in green!!!
wireframe 20 

echo Unpaired 3'-ending of tRNA is define as lends!

echo nucleotids of anticodon are define as anticodon!

select anticodon
color red
echo  GUA anticodon is in red!!!
wireframe 20 

pause
echo Ciao!