#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)

#--------------------------------------------------------------------------
#asn235 forms H-bonds with DNA
select dna
wireframe 100
select leu or arg
spacefill off
wireframe 100
select asn235
color green
spacefill 300
set echo top
color echo green
echo Focus on Asn 235
reset
rotate z -113
rotate y 2
rotate x -177
rotate y 90
center atomno=198
zoom 250
translate y -20