#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)

#--------------------------------------------------------------------------
#View H-bonds between 
#	Asn235c: OD1(909)  --  C12(chaina): N4(243)
#	         ND2(910)  --  T29(chainb): O4(589)
#(there is another set:
#	Asn235d: OD1(1390) --  C34(chainb): N4(694)
#	         ND2(1391) --  T7(chania):  O4(141))
restrict asn235c, 234c, 236c, c12, t29, g30, a13
color white
reset
rotate z 62
rotate y -10
rotate x -53
translate x 4
translate y -17
select asn235c, c12, t29
zoom 300
spacefill 300
color cpk
select atomno=909, atomno=243
color cpk
color monitor black
set monitor 2
monitor 243 909
monitor 589 910
select atomno=910, atomno=589
color cpk
center atomno=243
zoom 500
#
set fontsize 20
select c12.O2
label C12
select t29.O3*
label T29
select asn235c.N
label Asn235
set echo top
echo Read the H-bond Matrix
#select dna
#ribbon 300
#color yellow
#select protein and not asn235c
#ribbon 300
#color lightblue