# E. coli chemotaxis simulation file # for Fig.1 in Smoldyn2 paper (Andrews, Brent & Arkin'08) # CheYp/CheZ complexes as in Lipkow&Odde'08 # as zy40, but with motors and E.coli shape # time is in ms, length in 10 nm pixels graphics opengl_good graphic_iter 100000 # change this to 1000 or more when generating your figure dim 3 names A Ap mA mAp Y Yp Z ZYp ZYp2 M MYp max_mol 100000 molperbox 15 difc A 0 difc Ap 0 difc mA 0 difc mAp 0 difc Y 20 # 2 µm^2 s^-1 difc Yp 20 difc Z 20 difc ZYp 2 # 0.2 µm^2 s^-1 difc ZYp2 2 difc M 0 difc MYp 0 color A 0.6 0.6 0.45 # beige: CheA, inactive color Ap 1 1 0 # yellow: CheAp, inactive, phosphorylated color mA 1 0.5 0 # orange: CheA, active (m for 'methylated') color mAp 1 1 0 # yellow: CheAp, active, phosphorylated color Y 0 0 0 # black: CheY color Yp 1 0 0 # red: CheYp, phosphorylated color Z 0 0 1 # blue: CheZ2 color ZYp 0.5 0 0.5 # purple: CheZ2-CheYp color ZYp2 0.9 0 0.5 # magenta: CheZ2-CheYp2 color M 0 0.4 0 # dark green: FliM color MYp 0 1 0 # light green: FliM-CheYp display_size A 0.5 # monomers and homodimers: small display_size Ap 0.5 display_size mA 0.5 display_size mAp 0.5 display_size Y 0.5 display_size Yp 0.5 display_size Z 0.5 display_size ZYp 0.8 # heterodimers and multimers: large display_size ZYp2 0.8 display_size M 0.8 display_size MYp 1.2 frame_thickness 0 time_start 0 time_stop 10000 # 10 s is a good time to take a picture: cell reaches steady state and the final gradient at c. 9 s time_step 0.1 boundaries 0 -50 230 r boundaries 1 -50 50 r boundaries 2 -50 50 r read_file posE_M_49 max_surface 1 start_surface name ecoli action both all reflect color front 0.6 0.6 0.7 polygon both edge #polygon front face thickness 4 max_panels cyl 1 panel cyl 0 0 0 180 0 0 -50 30 10 max_panels hemi 2 panel hemi 0 0 0 -50 1 0 0 30 10 panel hemi 180 0 0 -50 -1 0 0 30 10 end_surface max_compartment 1 start_compartment name inside surface ecoli point 90 0 0 end_compartment compartment_mol 8200 Y inside read_file posE_A_48_1.5_1276 compartment_mol 1600 Z inside #output_files out2.txt #cmd b pause cmd i 0 20000 10 equilmol A mA 0.132 cmd i 0 20000 10 equilmol Ap mAp 0.132 #cmd i 0 20000 100 molcount out2.txt reaction ah3 mA -> mAp 3.4e-2 # mA -> mAp 34 s^-1 reaction z3 ZYp -> Yp + Z 5e-4 # ZYp -> Yp + Z 0.5 s^-1 product_placement z3 pgemmax 0.2 reaction z4 ZYp -> Y + Z 5e-3 # ZYp -> Y + Z 5 s^-1 reaction z5 ZYp2 -> Yp + ZYp 5e-4 # ZYp2 -> Yp + ZYp 0.5 s^-1 product_placement z5 pgemmax 0.2 reaction z6 ZYp2 -> Y + ZYp 5e-3 # ZYp2 -> Y + ZYp 5 s^-1 reaction m2 MYp -> M + Yp 2e-2 # MYp -> M + Yp 20 s^-1 product_placement m2 pgemmax 0.2 reaction ah21 Y + Ap -> Yp + A 1.66e2 # Y + Ap -> A + Yp 1e8 M^-1 s^-1 reaction ah22 Y + mAp -> Yp + mA 1.66e2 # Y + mAp -> mA + Yp 1e8 M^-1 s^-1 reaction z2 Yp + Z -> ZYp 3.32e1 # Yp + Z -> ZYp 2e7 M^-1 s^-1 reaction z7 Yp + ZYp -> ZYp2 1.66e1 # Yp + ZYp -> ZYp2 1e7 M^-1 s^-1 reaction m1 Yp + M -> MYp 8.3e0 # Yp + M -> MYp 5e6 M^-1 s^-1 end_file