#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
select arg or leu
spacefill off
select dna
color cyan
wireframe 100
backbone 100
select all
restrict within(15.0,asn235)
select (within(15.0,asn235) and not within(10.0,asn235))
color grey
wireframe 50
select within(10.0, asn235)
reset
rotate z 40
rotate y -24
rotate x -60
translate x -14
translate y -21
select asn235
spacefill 300
color green
select c12, c34, t29, t7
color cpk
wireframe 150
select atomno=909, atomno=243, atomno=1390, atomno=694
spacefill 300
color red
select atomno=910, atomno=589, atomno=1391, atomno=141
spacefill 300
color purple
select protein and within(10.0, asn235) and not asn235 
color orange
set echo top
echo Symmetric major groove interactions
center atomno=243
zoom 250