# Script for display of 1lmb.pdb, the lambda repressor at 1.8 A, from
# Beamer and Pabo, 1992, JMB 227, 177-196.  
# Rasmol commands by Jason Kahn, UMCP
# If you haven't loaded the molecule yet:
#zap
#load 1lmb.pdb
#
set ambient 60
set specular on
set shadows on
reset
rotate z 51
rotate y 11
rotate x -74
select all
hbonds
hbonds 40
color hbonds green
hbonds 41
define halfdna (dna and (resno>10 and resno<32))
define halfall (halfdna or (resno<61 and :4))
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 u_major (U and (*.C5 or *.O4 or *.C4 or *.H5))
define major_groove (g_major or a_major or c_major or t_major or u_major)
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 u_minor (U and (*.C2 or *.O2))
define minor_groove (g_minor or a_minor or c_minor or t_minor or u_minor)
select all
wireframe 50
select protein
color cpk
cartoons on
#
# Identify first helix of HTH motif in red
#
select (resno>32 and resno<40 and protein)
color red                                 
#
# Identify turn of HTH motif in blue
#
select (resno>39 and resno<44 and protein)
color blue
#
# Identify recognition helix of HTH motif in blue
#
select (resno>43 and resno<52 and protein)
color purple
#
# Identify N-terminal arm in orange
#
select (resno<8 and protein)
color orange
#
# Identify dimerization helix in green
#
select (resno>78 and protein)
color green
select dna
wireframe 150
backbone 300
color backbone cyan
#
# identify DNA grooves
#
select major_groove
color red
select minor_groove
color blue
# Now spin around etc. as you please
reset
rotate z 51
rotate y 11
rotate x -74
# Zoom in one half-site
zoom 140
translate y 26
select all
hbonds off
restrict halfall
select halfall
hbonds on
hbonds 30
center (atomno=1844)                      
wireframe 80
select dna and halfall
wireframe 150
select halfall
#
# Look at space filling model
#
spacefill
set shadows off
set specular off
select protein and halfall
color [50,50,50]
#
# highlight Q33-Q44-T23-A24 interaction in the half site
# Gln33 is part of the first HTH helix, Q44 part of the
# official recognition helix.  This is taken from figure 6
# of the paper.  Two bridging water molecules are in yellow
#
select halfall
spacefill off
reset
rotate z 51
rotate y 11
rotate x -74
zoom 140
translate y 26
set shadows on
set specular on
hbonds off    
cartoons off
backbone off
select (resno>43 and resno<52 and :4)
cartoons
color purple
select (:4 and (gln44 or gln33))
color green
wireframe 150
select (T23 or A24)
wireframe 150
color cyan
select (HOH17 or HOH90)
color yellow
spacefill
#Now zoom in on the interaction
reset
restrict ((:4 and (gln44 or gln33)) or T23 or A24 or HOH90 or HOH17 or atomno=436)
color cpk
zoom 400
translate x 50
translate y -10
set fontsize 12
select gln44 and :4 and *.CA
label %n%r
select gln33 and :4 and *.CA
label %n%r
select HOH17 or HOH90
color yellow
select all
monitors off
set monitors off
monitor 1835 1757
monitor 1835 482
monitor 1834 485
monitor 1758 470
monitor 465 2215
monitor 2286 1834
monitor 2286 2215
color monitors green
center atomno=466
# zoom in on phosphate network [to be done later]
#