# This is a Rasmol script to demonstrate tRNA structure 1qu3.
# In order to automatically load PDB file you may insert the following line
# load 1qu3.pdb      
# Be careful with directories and paths!
#
# You may include all definitions in a separate file 1qu3.def and in this script
# just add a line
# script 1qu3.def
#
define   helix1   1-7, 66-72
define   helix2  10-13, 22-25
define   helix3   26-31, 39-44
define   helix4    49-53, 61-65


define helixes  helix1,helix2, helix3, helix4
echo tRNA helices 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  14-21
define loop2   32-38
define loop3  45-48
define loop4  54-60


define loops loop1,loop2,loop3,loop4

echo For loops were just given the following names:
echo loop1 - for D-loop
echo loop2 - for anticodon loop
echo loop3 - for variable loop
echo loop4 - for T-loop
define lends 74-75

define knot1  5,68
define knot2 26,44
define knot3  49, 65
define knot4 8,14
define knot5  15,48
define knot6 19,56
define knot7  18,55
define knots knot1, knot2, knot3,knot4, knot5, knot6, knot7

define lends 73,74
echo Unpaired 3'-ending of tRNA is define as lends

define anticodon 34-36
echo 3 nucleotides of anticodon loop are now define as anticodon!

center 23
rotate x 60
rotate y -70  

restrict rna
color white
backbone 50

select helix1
color blue
select helix2
color violet
select helix3
color green
select helix4
color pink



restrict none
select all 
wireframe 80


pause        
select knots
color yellow
echo Non-canonical pairs are in yellow.
select anticodon
color red
echo  GAU anticodon is in red.
pause