Config Files - Hands

hand_track.cym

/**
 @example hand_track.cym
 We create a Tracker with `hand:activity=track`

 F. Nedelec, June 2011
*/


set simul hand_track 
{
    time_step = 0.005
    viscosity = 0.02
}

set space cell
{
    geometry = ( capsule 10 2 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    confine = inside, 500
    display = { line_width=1; minus_end=4, 8; }
}

new 1 fiber microtubule
{
    length = 19
    position = ( 0 0 0 )
}

set hand tracker
{
    binding_rate = 10
    binding_range = 0.1
    unbinding_rate = 0.1
    unbinding_force = 10
    
    activity = track
    bind_end = plus_end, 1
    display = { width=3; size=6; color=green }
}

set single protein
{
    hand = tracker
    diffusion = 10
}

new 1000 single protein

run simul *
{
    nb_steps = 40000
    nb_frames = 50
}

hand_cut.cym

/**
 @example hand_cut.cym
 We create a Cutter with `hand:activity=cut`

 F. Nedelec, October 2011
*/


set simul hand_cut 
{
    time_step = 0.005
    viscosity = 0.1
}

set space cell
{
    geometry = ( sphere 5 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.25
    confine = inside, 100
}

new 1 fiber microtubule
{
    length = 10
    position = ( 0 0 0 )
}


set hand cutter
{
    binding_rate = 10
    binding_range = 0.05
    unbinding_rate = 0
    unbinding_force = 3
    activity = cut
    cutting_rate = 10
    display = { size=8; color=green; }
}

set single protein
{
    hand = cutter
    diffusion = 1
}

new 100 single protein

run simul *
{
    nb_steps = 5000
    nb_frames = 10
}

hand_slide.cym

/**
 @example hand_slide.cym
 We create a Slider with `hand:activity=slide`

 F. Nedelec, June 2011
*/

set simul hand_slide 
{
    time_step = 0.005
    viscosity = 0.02
}

set space cell
{
    geometry = ( sphere 10 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    confine = inside, 500
    display = { line_width=3; minus_end=4, 8; }
}

new 1 fiber microtubule
{
    length = 19
    position = ( 0 0 0 )
}

set hand slider
{
    binding_rate = 10
    binding_range = 0.01
    unbinding_rate = 0.1
    unbinding_force = 10
    
    activity = slide
    mobility = 1
    stiffness = 100
    display = { width=3; size=6; color=green }
}

set single protein
{
    hand = slider
    activity = fixed
    stiffness = 100
}

new 100 single protein

run simul *
{
    nb_steps = 40000
    nb_frames = 50
}

hand_move.cym

/**
 @example hand_move.cym
 We create a Motor with `hand:activity=move`

 F. Nedelec, April 2010
*/

set simul hand_move
{
    time_step = 0.005
    viscosity = 0.02
}

set space cell
{
    geometry = ( sphere 10 )
}

new space cell

set fiber microtubule
{
    rigidity = 30
    segmentation = 0.5
    confine = inside, 500
    display = { line_width=2; minus_end=4, 8; }
}

new 1 fiber microtubule
{
    length = 19
    position = ( 0 0 0 )
}

set hand motor
{
    binding_rate = 10
    binding_range = 0.05
    unbinding_rate = 0.2
    unbinding_force = 3
    hold_growing_end = 1
    
    activity = move
    max_speed = 1
    stall_force = 5
    display = { width=3; size=12; color=green }
}

set single protein
{
    hand = motor
    diffusion = 0.1
}

new 100 single protein

run simul *
{
    nb_steps = 40000
    nb_frames = 50
}

hand_walk.cym

hand_nucleate.cym

/**
 @example hand_nucleate.cym
 We create a Nucleator with `hand:activity=nucleate`

 F. Nedelec, April 2011
*/

set simul hand_nucleate 
{
    time_step = 0.005
    viscosity = 10
}

set space cell
{
    geometry = ( capsule 3 1 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    confine = inside, 100
}

new 1 fiber microtubule
{
    length = 5
    position = ( 0 0 0 )
    orientation = horizontal
}

set hand activator
{
    binding_rate = 1
    binding_range = 0.05
    unbinding_rate = 0
    unbinding_force = 3
    display = { size=8; color=white; }
}

set hand nucleator
{
    unbinding_rate = 0
    unbinding_force = 3
    activity = nucleate
    nucleate = 10, microtubule, ( fiber_length=1; )
    specificity = parallel
    display = { size=10; color=green; }
}

set couple complex
{
    hand1 = activator
    hand2 = nucleator
    diffusion = 1
    stiffness = 100
    activity = crosslink
    length = 0.1
    trans_activated = 1
}

new 1000 couple complex

run simul *
{
    nb_steps = 5000
    nb_frames = 10
}

hand_rescue.cym

/**
 @example hand_rescue.cym
 We create a Rescuer with `hand:activity=rescue`

 F. Nedelec, September 2012
*/

set simul rescue
{
    time_step = 0.01
    viscosity = 1
}

set space cell
{
    geometry = ( capsule 2 2 )
}

new space cell

set fiber microtubule
{
    rigidity     = 20
    segmentation = 0.5
    confine      = inside, 200
    
    activity        = dynamic
    unit_length     = 0.008
    growing_speed   = 0.06
    shrinking_speed = -0.15
    hydrolysis_rate = 0.25
    growing_force   = 1.7
    display = { line_width=2; plus_end=16, 2; }
}

new 5 fiber microtubule
{
    length = 5
    end_state = red
}

set hand rescue
{
    binding_rate = 10
    binding_range = 0.1
    unbinding_rate = 0.1
    unbinding_force = 10
    
    activity = rescue
    rescue_prob = 0.1
    display = { width=3; size=6; color=green }
}

set single protein
{
    hand = rescue
    diffusion = 10
}

new 500 single protein

run simul *
{
    nb_steps = 100000
    nb_frames = 10
}