#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)

#--------------------------------------------------------------------------
#Positive arginine residues interact with negative DNA backbone
select arg
color blue
spacefill 300

set echo top
color echo blue
echo Arginine in blue
reset
rotate z -113
rotate y 2
rotate x -177
rotate y 90