#This script is for display of GCN4, a yeast transcription 
#factor containing a basic region leucine zipper (bZIP) DNA-binding motif.
#From the structure determined by Ellenberger et al., 1992, Cell 71, pp.
# 1223-1237.  Rasmol commands by Hannah Chen, Jmol by Jason Kahn.
#If molecule isn't loaded...
#zap
#load GCN4-1.pdb
#Script starts here:
define g_major (G and (*.N7 or *.O6 or *.C5 or *.C6 or *.C8 or *.H8))
define a_major (A and (*.N6 or *.N7 or *.C5 or *.C6 or *.2H6 or *.C8 or *.H8)) 
define t_major (T and (*.C5 or *.O4 or *.C4 or *.C5M or *.1H5M or *.2H5M or *.3H5M))
define c_major (C and (*.C5 or *.N4 or *.C4 or *.1H4 or *.2H4 or *.H5))
define g_minor (G and (*.N3 or *.C4 or *.C2 or *.N2 or *.1H2 or *.2H2))
define a_minor (A and (*.N3 or *.C4 or *.C2 or *.H2))
define c_minor (C and (*.C2 or *.O2))
define t_minor (T and (*.C2 or *.O2))
define major_groove (g_major or a_major or c_major or t_major)
define minor_groove (g_minor or a_minor or c_minor or t_minor)

#-------------------------------------------------------------------------
select all
hbonds off
reset
restrict arg118,asp120,g10,c53
ribbon off
zoom 230
rotate z 4
rotate y 13
rotate x -109
translate x 26
wireframe 200
select (arg118,asp120,g10,c53) and not carbon
color cpk
select arg118.nh1, arg118.nh2, arg118.ne
spacefill 250
color blue
select asp120.od1, asp120.od2
spacefill 250
color magenta
select g10.n7, g10.o6, g10.n1, g10.n2
spacefill 250
select g10.o6
color magenta
select g10.n7, g10.n1, g10.n2
color blue
select c53.o2, c53.n3, c53.n4
spacefill 250
select c53.o2
color magenta
select c53.n3, c53.n4
color blue

set fontsize 16
select g10.o5*
label G10
select c53.p
label C53
select arg118.nh2
label Arg118
select asp120.od2
label Asp120
center atomno=938
select all
monitors off
set monitors off
monitor 938 144
monitor 935 143
monitor 158 144
monitor 141 157
color monitors green
select arg118,asp120,g10,c53
hbonds
hbonds 40
color hbonds green
#--------------------------------------------------------------------------