#
# Script for use with the HTML file "Make a covalent bond.html"
#
#  First hide all atoms, then display the residues of interest
#
HIDE *
display 1, 37, 38
zoom 0
delay 2
#
#   The 
#
#   Create a bond between the hydrogen and the ortho carbon,
#   and delete the bond from the hydrogen to the oxygen
#
connect (atomno=6) (atomno=530) single
connect (atomno=12) (atomno=528) single
connect (atomno=12) (atomno=6) delete
delay 2
minimize SELECT (1, 38) 
select (1, 38)
#
#  Run the command "write PDB" in the JSmol console after the minimize has finished
#
#  The coordinates of the selected atoms will appear in the console.
#  Copy them to the appropriate location.
#