# This is a Rasmol script to demonstrate tRNA structure 1j2b.pdb
# In order to automatically load PDB file you may insert the following line
# load 1j2b.pdb      
#

define   helix1   901-907, 967-977 and *c
define   helix2   908-923 and *c
define   helix3   924-949 and *c
define   helix4   950-966 and *c
define helices  helix1, helix2, helix3, helix4
echo tRNA helices are defined as helix1, helix2, helix3, helix4   
echo "helices" is for joint of helix1, helix2, helix3, helix4 

#Loop1 not exist
define loop2  934-938 and *c
define loop3  956-958 and *c
echo tRNA loops are defined as loop2, loop3   


define knot1  928, 945 and *c
define knot2  933, 937 and *c
echo tRNA non wc pair are defined as knot1, knot2   

define lends  901, 977 and *c
define anticodon 935-937 and *c
echo tRNA 5' and 3' ands are defined as lends   


restrict none
select *c
wireframe 150
select helix1
color red
select helix2
color blue
select helix3
color yellow
select helix4
color green


pause  

     
select knot1, knot2
color cyan
echo Non-canonical pairs are in cyan.
select anticodon
color purple
echo Anticodon is in purple.


pause


select protein
wireframe 150
color grey