# PAgfp (CaMKa) diffusion with basic dendrite & spine architecture. 
# Excluded volume spine and stalk centers.

graphics opengl_better
graphic_iter 10
accuracy 1
#tiff_iter 1000
#tiff_name basic

dim 3
names CaMKa CaMKb NR2B PSDA PSDB
#output_files data1.txt data2.txt
max_mol 50000

difc CaMKa 275
difc CaMKb 275
difc NR2B 0.0
difc PSDA 0.0
difc PSDB 0.0

#color CaMKa 0.4 0.2 0.1	# brown
color CaMKa 0 1 0		# green
color CaMKb 0 1 0		# green
color NR2B 1 0.8 0.3		# yellow
#color PSDA 0.4 0.2 0.1		# brown
color PSDA 0 1 0		# green
color PSDB 0 1 0		# green

display_size all(all) 1.5
light 0 position -1000 1000 -100
light 0 diffuse 1 1 1
light 0 specular 1 1 1
background_color 0 0 0
frame_thickness 0

time_start 0
time_stop 10000
time_step 1

low_wall 0 -250 r
high_wall 0 250 r
low_wall 1 -250 r
high_wall 1 250 r
low_wall 2 -250 r
high_wall 2 250 r


# The dendrite is modeled as a rectangle with two bounding plates
# It runs along the x-axis
mol 1250 CaMKa 250--250 45-35 45-35		# a stripe the length of the stalk
mol 1250 CaMKa 250--250 -35--45 -35--45		# another stripe in the stalk
mol 500 CaMKa 50--50 50--50 -190--100		# random within the spine head
mol 10 CaMKa 5--5 50--50 50--50			# random within the middle of the stalk
mol 300 NR2B 50--50 50--50 -190--200		# at the PSD
mol 5 PSDA 50--50 50--50 -190--200		# at the PSD


max_surface 5

start_surface
name stalk1			# right side of stalk
action both all r
#color both 0.9 0.4 0.2 0.3
color both 1 1 1
thickness 2
polygon both edge
#polygon both face

max_panels r 20
panel r +1 -250 -50 -50 500 100 r1	# y side of stalk
panel r +1 20 -50 -50 -40 -50 r9	# narrow portion of neck
panel r +1 50 -50 -100 -100 -100
panel r -2 -250 -50 50 500 100 r3	# solid z side of stalk
panel r +2 -250 -50 -50 230 100 r4	# part z side of stalk
panel r +2 20 -50 -50 230 100 r5	# part z side of stalk
panel r -0 20 50 -50 -100 -50 r6	# wide portion of neck
panel r -0 -20 50 -50 -100 -50 r7	# wide portion of neck
panel r -0 50 50 -100 -100 -100		# head of spine
panel r -0 -50 50 -100 -100 -100
panel r -1 50 50 -100 -100 -100
panel r -2 50 50 -200 -100 -100
panel r -2 50 50 -100 -30 -100
panel r -2 -50 50 -100 30 -100
panel r -1 -250 50 -50 500 100 r2	# y side of stalk
panel r -1 20 50 -50 -40 -50 r8		# narrow portion of neck


end_surface


start_surface			# plates at either end of stalk
name reflectStalk
action both CaMKa a
action both CaMKb a
color both 0 0 0
thickness 0
polygon both edge
max_panels r 2
panel r -0 250 -60 -60 120 120
panel r +0 -250 -60 -60 120 120
end_surface



cmd b pause


#cmd i 0 6000 1 excludebox -40 40 -40 40 -155 -125
#cmd i 0 6000 1 excludebox -250 250 -15 15 -30 30
#cmd @ 100 replacevolmol CaMKa CaMKb 1 -50 50 -50 50 -50 50
#cmd @ 100 replacevolmol PSDA PSDB 1 -50 50 -50 50 -50 50
#cmd i 0 10000 100 listmols3 CaMKb data1.txt
#cmd i 0 10000 100 listmols3 PSDB data2.txt

end_file