# Measure effect of distance between loci on translocations. 1st order repair kinetics
# Units are microns and seconds


graphics opengl

dim 3

define site1 0.5 0.5 0.5
define site2 0.5 0.75 0.5

species Brk1 Brk2 Ligated1 Ligated2 Translocated    


#define how the "molecules" move

difc Brk1 0.00002
difc Brk2 0.00002
difc Ligated1 0
difc Ligated2 0
difc Translocated 0


#define how the "molecules" look in the graphics

color Brk1 blue
display_size Brk1 10

color Ligated1 darkblue
display_size Ligated1 10	

color Brk2 red
display_size Brk2 10
	
color Ligated2 darkred
display_size Ligated2 10

color Translocated green
display_size Translocated 10


#define the time parameters

time_start 0
time_stop 24000
time_step 0.001


#define the simulation volume
boundaries 0 -5 5
boundaries 1 -5 5
boundaries 2 -5 5


#create the nucleus
start_surface nucleus
action both all reflect
color both 0.3 0.3 0.3	
polygon both edge
max_panels sphere 1
panel sphere 0 0 0 2.5 20 20
end_surface


#tells the simulation to wait until I press the spacebar before it starts
cmd b pause


# set the number and position of molecules 
#"number" "name" "coordinates x y z"

mol 1 Brk1 site1
mol 1 Brk2 site2


#define the reactions
#reaction "name" "reactants" -> "products" "rate"

reaction rep1 Brk1 -> Ligated1 .001
reaction rep2 Brk2 -> Ligated2 .001
reaction trans Brk1 + Brk2 -> Translocated 0.00002

cmd n 2400000 pause
cmd n 2400000 killmol all   
cmd n 2400000 set mol 1 Brk1 site1
cmd n 2400000 set mol 1 Brk2 site2

end_file


