# Animated cartoon of signaling

graphics opengl
graphic_iter 1

dim 3
boundaries x -10 10
boundaries y -10 10
boundaries z -10 10

species Receptor ReceptorActive Pheromone Messenger MessengerActive DNA RNAActive GFPActive

difc Receptor*(up) 1
difc all(soln) 100

color Receptor(up) maroon
color ReceptorActive(up) fuchsia
color Pheromone black
color Messenger brown
color MessengerActive orange
color DNA blue
color RNAActive violet
color GFPActive green

display_size all(all) 3
display_size *Active(all) 7

time_start 0
time_stop 100
time_step 0.0001

frame_thickness 0

start_surface bounds
action both all transmit
polygon both none
panel sphere 0 0 0 10 20 20
end_surface

start_surface cell
action both all reflect
color both grey
polygon both edge
panel sph 0 0 0 5 30 30
end_surface

start_surface nucleus
action both DNA reflect
action both RNAActive transmit
action both GFPActive transmit
rate Messenger soln bsoln 10
rate Messenger bsoln soln 10
color both blue
polygon both edge
panel sphere 1 1 1 2 20 20
end_surface

reaction r1 Pheromone + Receptor(up) -> ReceptorActive(up) 100
reaction r2 ReceptorActive(up) -> Receptor(up) 1

reaction r3 ReceptorActive(up) + Messenger(bsoln) -> ReceptorActive(up) + MessengerActive(bsoln) 100
reaction r4 MessengerActive + DNA -> Messenger + DNA + RNAActive 1000

reaction r5 RNAActive -> 0 1
reaction r6 RNAActive -> GFPActive 10




start_compartment nucleus
surface nucleus
point 2 2 2
end_compartment

start_compartment cell
surface cell
point 0 0 0
compartment andnot nucleus
end_compartment

compartment_mol 1 DNA nucleus
compartment_mol 500 Messenger cell
surface_mol 500 Receptor(up) cell all all

mol 100 Pheromone 9.5 0 0

cmd b pause

text_display GFPActive

end_file



