Example model files for Magrathea

Copy and paste any of the examples below to a file named model.txt and move to the same directory as magrathea.tz to run.

Example 1. Point coordinator representing an interaction

###########
#interaction.1.txt
#showing a coordinator used to model an interaction between two molecules
#
#last tested with breve 2.6.1 and magrathea.tz 1.40
###########


[simulation]
camera-at-from 10 10 0 0 1 30
light-source 0 20 20
movie-length 10
[/simulation]

[moleculeType]
id 1
label a
show-label 1
color .81 .60 .21
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 3
instantiate 1 random spherical volume 10 10 0 1
[/moleculeType]

[moleculeType]
id 2        
label b
show-label 1
color 0.67 0.08 0.37
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 3
instantiate 1 random spherical volume 15 10 10 1
[/moleculeType]

[coordinatorType]
id 3
label complex
shape Cube 1 1 1
neighborhood-size 1
molecule 1 1
molecule 2 1
[/coordinatorType]

#****************************************************************

EOF

Example 2. Point coordinator representing a complex

###########
#complex.1.txt
#showing a coordinator used to model a complex between three molecules
#complex stoichiometry is a,b,c (note one extra c molecule is left out)
#last tested with breve 2.6.1 and magrathea.tz 1.42
###########


[simulation]
camera-at-from 10 10 0 0 1 30
light-source 0 20 20
movie-length 10
[/simulation]

[moleculeType]
id 1
label a
show-label 1
color .81 .60 .21
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 4
instantiate 1 random spherical volume 10 10 0 1
[/moleculeType]

[moleculeType]
id 2        
label b
show-label 1
color 0.67 0.08 0.37
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 4
instantiate 1 random spherical volume 15 10 10 1
[/moleculeType]

[moleculeType]
id 3        
label c
show-label 1
color 0.47 0.11 0.37
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 4
instantiate 2 random spherical volume 5 10 10 1
[/moleculeType]


[coordinatorType]
id 4
label complex
shape Cube 1 1 1
neighborhood-size 1
molecule 1 1
molecule 2 1
molecule 3 1
[/coordinatorType]

#****************************************************************

EOF

###########
#complex.2.txt
#showing a coordinator used to model a complex between four molecules
#stoichiometry of complex is a,b,2c
#last tested with breve 2.6.1 and magrathea.tz 1.42
###########


[simulation]
camera-at-from 10 10 0 0 1 30
light-source 0 20 20
movie-length 10
[/simulation]

[moleculeType]
id 1
label a
show-label 1
color .81 .60 .21
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 4
instantiate 1 random spherical volume 10 10 0 1
[/moleculeType]

[moleculeType]
id 2        
label b
show-label 1
color 0.67 0.08 0.37
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 4
instantiate 1 random spherical volume 15 10 10 1
[/moleculeType]

[moleculeType]
id 3        
label c
show-label 1
color 0.47 0.11 0.37
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 4
instantiate 2 random spherical volume 5 10 10 1
[/moleculeType]


[coordinatorType]
id 4
label complex
shape Cube 1 1 1
neighborhood-size 1
molecule 1 1
molecule 2 1
molecule 3 2
[/coordinatorType]

#****************************************************************

EOF

Example 3. Point coordinator representing a compartment

###########
#compartment.1.txt
#showing a coordinator used to model a compartment with 20 
#closely packed "surface" molecules
#one coordinator type is used with one molecule type
#
#last tested with breve 2.6.1 and magrathea.tz 1.42
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]
camera-at-from 10 10 0 0 1 30
light-source 0 20 20
movie-length 10
[/simulation]

[moleculeType]
id 1
label a
show-label 0
color .81 .60 .21
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 2
instantiate 20 random spherical volume 10 10 0 1
[/moleculeType]



[coordinatorType]
id 2
label compartment
shape Sphere 0.1
opacity 0.5
geometricType point
neighborhood-size 5
#
isSizeDynamic 1
#
molecule 1 20
[/coordinatorType]

#****************************************************************

EOF

###########
#compartment.2.txt
#showing a coordinator used to model a compartment with 20 
#surface marker molecules
#the actual diameter of these marker molecules is larger than what is 
#rendered using the line
#shape Sphere 1 2
#one coordinator type is used with one molecule type

#last tested with breve 2.6.1 and magrathea.tz 1.42
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]
camera-at-from 10 10 0 0 1 30
light-source 0 20 20
movie-length 10
[/simulation]

[moleculeType]
id 1
label a
show-label 0
color .81 .60 .21
#
shape Sphere 1 2
#
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 2
instantiate 20 random spherical volume 10 10 0 1
[/moleculeType]



[coordinatorType]
id 2
label compartment
shape Sphere 0.1
opacity 0.5
geometricType point
neighborhood-size 5
isSizeDynamic 1
molecule 1 20
[/coordinatorType]

#****************************************************************

EOF

Example 4. Plane coordinator representing a membrane section.

###########
#membrane.1.txt
#showing a coordinator used to model a membrane section 
#20 member molecules are moved to the surface of the plane and 
#their random movement is constrained to the surface of this plane
#
#last tested with breve 2.6.1 and magrathea.tz 1.42
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]
camera-at-from 10 10 0 0 1 50
light-source 0 20 20
movie-length 15
[/simulation]

[moleculeType]
id 1
label a
show-label 0
color .81 .60 .21
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 2
instantiate 20 random spherical volume 10 10 0 5
[/moleculeType]



[coordinatorType]
id 2
label membrane
color .383 .466 .561
opacity 0.5
shape Cube 30 .2 30
geometricType plane
neighborhood-size 5
#
isCreationDynamic 0
isMobile 0
isSizeDynamic 1
#
molecule 1 20
#orientation vertex 0 1 0 pointing-at 0 1 0
#orientation vertex 0 1 0 pointing-at 1 0 0
#orientation vertex 0 1 0 pointing-at 0 0 1
instantiate 1 determined point - 10 5 10
[/coordinatorType]

#****************************************************************

EOF

###########
#membrane.2.txt
#showing a coordinator used to model a membrane section 
#20 member molecules are moved to the surface of the plane and 
#their random movement is constrained to the surface of this plane
#non-membrane molecules (molecule type 2) will collide and be reprelled
#by the surface of this planar coordinator
#
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]
camera-at-from 10 10 0 0 1 50
light-source 0 20 20
movie-length 15
[/simulation]

[moleculeType]
id 1
label compartment_marker
show-label 0
color .81 .60 .21
shape Sphere .5 2
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
coordinator 1 3
instantiate 20 random spherical volume 10 10 10 5
[/moleculeType]

[moleculeType]
id 2
label non_membrane_molecule
show-label 0
color .37 .51 .26
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1.0
dynamic-neighborhood-sizing 1
instantiate 20 random spherical volume 10 15 10 5
instantiate 20 random spherical volume 10 5 10 5
[/moleculeType]


[coordinatorType]
id 3
label membrane
color .383 .466 .561
opacity 0.5
shape Cube 30 .2 30
geometricType plane
neighborhood-size 5
isCreationDynamic 0
isMobile 0
isSizeDynamic 1
molecule 1 20
#orientation vertex 0 1 0 pointing-at 0 1 0
#orientation vertex 0 1 0 pointing-at 1 0 0
#orientation vertex 0 1 0 pointing-at 0 0 1
instantiate 1 determined point - 10 10 10
[/coordinatorType]

#****************************************************************

EOF

Example 5. Line coordinator representing a microtubule.

###########
#microtubule.1.txt
#showing a linear coordinator used to model a microtubule or some
#other linear macromolecular structure 
#20 member molecules are moved to the line coordinator and 
#their random movement is constrained to this line
#the line coordinator is dynamically sized so it grows in length 
#as molecules join it
#the molecules have an effective radius of 2 (versus the rendered 1 unit)
#so the molecules appear spaced out along the line
#
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]
camera-at-from 20 10 0 1 1 70
light-source 0 20 20
movie-length 40
[/simulation]

[moleculeType]
id 1
label line_coordinator_component_1
show-label 0
color .81 .60 .21
shape Sphere 1 2
show-neighbor-lines 1
neighborhood-size 1
dynamic-neighborhood-sizing 1
coordinator 1 2
instantiate 20 random cylindrical volume 10 15 10 0 1 0 0 35
[/moleculeType]



[coordinatorType]
id 2
label line_coordinator
color .383 .466 .561
opacity 1
shape Cube .2 .2 .2
geometricType line
neighborhood-size 5
isCreationDynamic 0
isMobile 0
isSizeDynamic 1
molecule 1 20

#various orientations to try
#remove the # sign in front of one of these lines
#orientation vertex 1 0 0 pointing-at 0 1 0
#orientation vertex 1 0 0 pointing-at 1 0 0
#orientation vertex 1 0 0 pointing-at 0 0 1
#
#orientation vertex 1 0 0 pointing-at 1 1 0
#orientation vertex 1 0 0 pointing-at 1 0 1
#orientation vertex 1 0 0 pointing-at 0 1 1
#orientation vertex 1 0 0 pointing-at 1 1 1
instantiate 1 determined point - 30 10 10
[/coordinatorType]

#****************************************************************

EOF

Example 6. Coordinators and rules.

Example 6.1

###########
#rules.1.txt
#a simple demonstration of the use of rules by coordinators
#this example shows a substrate (molecule 1) that undergoes 
#a state-change (phosphorylation) upon interaction with a 
#kinase (molecule 2) 
#
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]
camera-at-from 10 15 10 0 1 30
light-source 0 20 20
movie-length 40
[/simulation]



[moleculeType]
id 1
label substrate
show-label 1
color .81 .60 .21
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1
dynamic-neighborhood-sizing 1

###
#the following line is read as: 
#there is some feature with an identifier of 234
#and this feature is given the label of "Tyr234"
###
feature 234 Tyr234

#-----------------------------------------------------------------
#the following line is read as: 
#there is some feature with an identifier of 234
#and this feature may have the value of 0
#and this feature-value pair is given the label "unphosphorylated"
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
feature-state 234 0 unphosphorylated

#-----------------------------------------------------------------
#the following line is read as: 
#there is some feature with an identifier of 234
#and this feature may have the value of 1
#and this feature-value pair is given the label "phosphorylated"
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
feature-state 234 1 phosphorylated

coordinator 1 3
instantiate 1 determined point - 10 10 10
[/moleculeType]


[moleculeType]
id 2
label kinase
show-label 1
color .92 .32 .11
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1
dynamic-neighborhood-sizing 1
coordinator 1 3
instantiate 1 determined point - 10 20 10
[/moleculeType]


[coordinatorType]
id 3
label complex_with_rules
color 1 1 1
shape Cube 1 1 1
neighborhood-size 10
molecule 1 1 0
molecule 2 1 0
[rule]
#-----------------------------------------------------------------
#this rule describes the complex formation
#the first two "if" lines specify
#which molecules must be present for the rule to be executed
#the "then" line specifies what happens if the rule is executed and
#the "parameters" line specifies a probability that
#the rule will be executed should the conditions be met 
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
id 1
#-----------------------------------------------------------------
#the following line is read (from left to right)
#if present a "tag" of 1 will be used to refer to 
#molecule of type 1 (where 1 instance is present)
#that is not (0) assembled with this coordinator
#and does not (0) have a feature-state pair of 234.1
#i.e. feature 234 in state 1 
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
if 1.1.1.0.0.234.1
if 2.2.1.0

#-----------------------------------------------------------------
#the following line is read
#molecule(s) assigned with tag 1 (see if lines above)
#are allowed to begin asembly with the coordinator
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
then 1 begins-assembly
then 2 begins-assembly

#-----------------------------------------------------------------
#the following line indicates that the event 
#described by the "then" lines above
#will be executed with a probability of 1
#if the conditions specified in the "if"
#lines above are met
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
parameters p 1
[/rule]


[rule]
#-----------------------------------------------------------------
#this rule describes a state change of the substrate (molecule 1)
#generated by the presence of the kinase (molecule 2)
#the state change is visualized by a change of colour of 
#the substrate molecule
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
id 2
if 1.1.1.1.0.234.1 
if 2.2.1.1
#-----------------------------------------------------------------
#the following line is read as:
#the molecule with the tag of 1 (see first "if" line above)
#changes state such that
#feature 234 assumes state 1
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
then 1 changes-state-to 234.1
then 1 changes-colour-to .1:.32:.11
parameters p 1
[/rule]


[rule]
#-----------------------------------------------------------------
#this rule describes the idea that the substrate (molecule 1) 
#leaves the coordinator once it has been phosphorylated
#i.e. feature 234 has a state value of 1
#see the "Making Models" section of the Magrathea manual
#for more a more detailed explanation
#-----------------------------------------------------------------
#unbinding
#id 3
if 1.1.1.1.1.234.1
if 2.2.1.1
then 1 leaves-coordinator
then 2 leaves-coordinator
parameters p 1
[/rule]
[/coordinatorType] 



#****************************************************************

EOF

Example 6.2

###########
#rules.2.txt
#This demonstration shows a somewhat more complex use of rules to 
#demonstrate the process of lateral signalling.
#In this example, a ligand molecule binds to a membrane-bound receptor.  
#On binding, the receptor changes state (becomes activated) as indicated by 
#a colour change.  The receptor in this new state also gains the ability to 
#bind to and activate other membrane bound receptors.
#
#No new concepts are introduced in this model compared to the rules.1.txt
#example so there are few comments in the file.
#See the "Making Models" section of the Magrathea manual for more details
#on the syntax of each line
# 
#after a molecule x changes state, molecule x and all molecule types that might be coordinated 
#in some coordinator with molecule x have there neighborhood size reset
#turn on #show-neighbor-lines 1# to see how this happens
#
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]
camera-at-from 10 15 10 0 10 30
light-source 0 20 20
movie-length 20
[/simulation]


[moleculeType]
id 1
label receptor
show-label 1
color .81 .60 .21
shape Sphere 1
neighborhood-size 1
show-neighbor-lines 1
dynamic-neighborhood-sizing 1
feature 234 Tyr234
feature-state 2 0 unphosphorylated
feature-state 2 63 phosphorylated
coordinator 1 5
coordinator 2 4
coordinator 3 3
instantiate 20 random planar - 10 15 10 20 0 1 0
[/moleculeType]

[moleculeType]
id 2        
label ligand
show-label 1
color .92 .32 .11
shape Sphere .7
neighborhood-size 1
dynamic-neighborhood-sizing 1
coordinator 1 5
instantiate 1 determined point - 10 20 10 1
[/moleculeType]


[coordinatorType]
id 3
label membrane
color .383 .466 .561
opacity 0.3
geometricType plane
shape Cube 30 .2 30
neighborhood-size 10
molecule 1 20
isCreationDynamic 0
isMobile 0
orientation vertex 0 1 0 pointing-at 0 1 0
instantiate 1 determined point - 10 15 10
[/coordinatorType]


[coordinatorType]
id 4
label receptor-receptor-complex
color 1 1 1
shape Cube 1 1 1
neighborhood-size 10
molecule 1 2 0
[rule]
#formation
id 1
if 1.1.1.0.1.2.63
if 2.1.1.0.0.2.63
then 1 begins-assembly
then 2 begins-assembly
parameters p1 1
[/rule]
[rule]
#lateral activation
id 2
if 1.1.1.1.1.2.63
if 2.1.1.1.0.2.63
then 2 changes-state-to 2.63
then 2 changes-colour-to .1:.32:.11
parameters p1 1
[/rule]
[rule]
#unbinding
id 3
if 1.1.1.1.1.2.63
if 2.1.1.1.1.2.63
then 1 leaves-coordinator
then 2 leaves-coordinator
#parameters p3 0.15
parameters p1 1
[/rule]
[/coordinatorType]

[coordinatorType]
id 5
label receptor-ligand-complex
color 1 1 1
shape Cube 1 1 1
neighborhood-size 10
molecule 1 1 0
molecule 2 1 0
[rule]
#formation
id 1
if 1.1.1.0.0.2.63
if 2.2.1.0
then 1 begins-assembly
then 2 begins-assembly
parameters p4 0.2
[/rule]
[rule]
#ligand activation
id 2
if 1.1.1.1.0.2.63 
if 2.2.1.1
then 1 changes-state-to 2.63
then 1 changes-colour-to .1:.32:.11
parameters p5 1
[/rule]
[rule]
#unbinding
#id 3
if 1.1.1.1.1.2.63
if 2.2.1.1
then 1 leaves-coordinator
then 2 leaves-coordinator
parameters p6 0.2
[/rule]
[/coordinatorType]


#****************************************************************

EOF

Example 6.3

###########
#rules.3.txt
#This demonstration shows two coordinator and their rules that control translocation
#into and out of a spherical compartment represented by a third coordinator.
#
#In this example, blue molecules (ligand) bind to a surface receptor (black) and are 
#translocated INTO the compartment where they change color to yellow.  A state change in 
#the ligand molecules then allows them to bind a second receptor (grey) that translocates 
#them OUT OF the compartment.
#
#See the "Making Models" section of the Magrathea manual for more details
#on the syntax of each line
# 
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]

#camera-at-from 30 20 30 14 13 30
camera-at-from 30 20 30 7 6 15

light-source 0 20 20
movie-length 40
[/simulation]


[moleculeType]
id 1
label compartment_marker
color .81 .60 .21
#----------------------------------------------------
#The following line causes comparment markers to be
#drawn as points in order to simplify the 
#visualization.
#See the "Making Models" section of the Magrathea
#manual for more details.
#----------------------------------------------------
draw-as-point 1
shape Sphere .2 1
neighborhood-size 5
coordinator 1 3
instantiate 30 random spherical surface 30 20 30 3
[/moleculeType]


[moleculeType]
id 2
label pump_in
show-label 1
color .11 .00 .21
shape Sphere .2
neighborhood-size 1
dynamic-neighborhood-sizing 1
coordinator 1 3
coordinator 2 7
instantiate 2 random spherical surface 30 22 30 1
[/moleculeType]

[moleculeType]
id 5
label pump_out
show-label 1
color .51 .50 .51
shape Sphere .2
neighborhood-size 1
dynamic-neighborhood-sizing 1
coordinator 1 3
coordinator 2 8
instantiate 2 random spherical surface 30 20 32 1
[/moleculeType]


[moleculeType]
id 4
label ligand
color .12 .12 .91
show-neighbor-lines 0
shape Sphere .2 
neighborhood-size 1
dynamic-neighborhood-sizing 1
resident-compartment-type 0
coordinator 1 7
coordinator 1 8
instantiate 6 random spherical volume 30 24 30 1
[/moleculeType]


[coordinatorType]
id 3
label compartment
color .92 .32 .11
#----------------------------------------------------
#The following line can be changed to
#opacity 0.2
#in order to visualize molecules inside the
#compartment. 
#See the "Making Models" section of the Magrathea
#manual for more details.
#----------------------------------------------------
opacity 1
shape Sphere 0.1
isCompartment 1
neighborhood-size 20
isCreationDynamic 1
isMobile 0
isSizeDynamic 1
molecule 1 30
molecule 2 2
molecule 5 2
instantiate 1 determined point - 30 20 30 
[/coordinatorType]


[coordinatorType]
id 7
label pump_in_complex
shape Cube .2 .2 .2
molecule 4 1 0
molecule 2 1 0

[rule]
id 1
#-----------------------------------------------------------------
#load pump
#ligand will enter the compartment if it has not been there before
#The following line is read as:
#If present, a tag of 34 is assigned to molecule type 4 (ligand) 
#(1 instance) that is not assembled with the this pump_in coordinator (0)
#and it is not a resident of the compartment coordinator (0.99999.3)
#and it does not have feature 2 in state 65 (0.2.65).
#The next line is read as:
#If present, a tag of 35 is assigned to molecule type 2 (pump_in) 
#(1 instance) if it is not assembled with this pump_in coordinator (0)
#and if it is assembled as a component of the compartment (1.99999.3).
#See the "Making Models" section of the Magrathea manual for more
#details on the syntax of these rule lines.
#-----------------------------------------------------------------  
if 34.4.1.0.0.99999.3.0.2.65
if 35.2.1.0.1.99999.3
then 34 begins-assembly
then 35 begins-assembly
parameters p 1.0
[/rule]

[rule]
id 2
#-----------------------------------------------------------------
#translocation
#This rule handles the translocation of the ligand molecule
#once it has assembled with the pump_in molecule.
#
#A feature-state of the ligand is changed to indicate that the
#ligand molecule has entered the comparment using the line
#"then 34 changes-state-to 2.65".
#This state-change prevents the ligand from 
#re-entering the compartment after it has been pumped out
#(see the pump_out_complex coordinator and rule 1 of this 
#coordinator.
#
#Upon translocation, the ligand has its feature 99999 set to 3 
#(the id of the compartment coordinator) by the line
#"then 34 translocates-into-compartment-of-molecule 35".
#This feature-state change then allows the ligand molecule
#to assemble with the pump_out molecule as specified by the 
#condition line "if 34.4.1.0.1.99999.3"
#in rule 1 of the pump_out_comlex coordinator below.
#See the "Making Models" section of the Magrathea manual for more
#details on the syntax of these rule lines.
#-----------------------------------------------------------------
if 34.4.1.1.0.99999.3
if 35.2.1.1.1.99999.3 
then 34 changes-state-to 2.65
then 34 changes-colour-to 1:1:0
then 34 translocates-into-compartment-of-molecule 35
then 34 leaves-coordinator
parameters p 1.0
[/rule]
[/coordinatorType]

[coordinatorType]
id 8
#-----------------------------------------------------------------
#Rules encoded by this coordinator handle assembly with the pump_out
#molecule and the translocation out of the compartment represented by
#coordinator 3
#The rules are similar to those in coordinator 7 but effect the 
#reverse process.
#See the "Making Models" section of the Magrathea manual for more
#details on the syntax of these rule lines.
#-----------------------------------------------------------------
label pump_out_complex
shape Cube .2 .2 .2
molecule 4 1 0
molecule 5 1 0
[rule]
#load pump
id 1
if 34.4.1.0.1.99999.3
if 35.5.1.0.1.99999.3
then 34 begins-assembly
then 35 begins-assembly
parameters p 1.0
[/rule]
[rule]
#translocation
id 2
if 34.4.1.1.1.99999.3
if 35.5.1.1.1.99999.3
then 34 translocates-outof-compartment-of-molecule 35
then 34 leaves-coordinator
parameters p 1.0
[/rule]
[/coordinatorType]


[coordinatorType]
id 10
#-----------------------------------------------------------------
#This coordinator shows an example of using plane coordinators 
#in different orientations that act as bounding walls for the 
#simulation.
#See the "Making Models" section of the Magrathea manual for more
#details on the syntax of these rule lines.
#-----------------------------------------------------------------
label simulation-container
color .383 .466 .561
opacity 0.1
geometricType plane
shape Cube 100 .2 100
neighborhood-size 10
isCreationDynamic 0 
isMobile 0
#west wall
orientation vertex 0 1 0 pointing-at 1 0 0
instantiate 1 determined point  - 0 50 50
#east wall
orientation vertex 0 1 0 pointing-at -1 0 0
instantiate 1 determined point  - 100 50 50
#north wall
orientation vertex 0 1 0 pointing-at 0 0 1
instantiate 1 determined point  - 50 50 0
#south wall
orientation vertex 0 1 0 pointing-at 0 0 -1
instantiate 1 determined point  - 50 50 100
#sky wall
#ground wall
[/coordinatorType]


EOF

Example 6.4

###########
#rules.4.txt
#
#translocation demonstration
#In this example, a blue particle (ligand) binds to a surface receptor and is translocated past the
#membrane (mediated by the black receptor) where it changes color to yellow.  
#Once on the other side of the membrane, the particle may then bind a second
#receptor (grey) that translocates it back to the top of the membrane
#Use of the two different receptors for translocation "in and out" is controlled by
#a feature-state pair.
#Planar coordinators are not compartments in the sense that molecules can move in and out of them.
#Instead, they represent barriers within a compartment (in this case the simulation)
#that molecules can move past with the help of a mediator molecule (the black and grey receptors).
#
#See the "Making Models" section of the Magrathea manual for more details
#on the syntax of each line
# 
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]

#camera-at-from 30 20 30 14 13 30
camera-at-from 30 20 30 7 6 15

light-source 0 20 20
movie-length 40
[/simulation]


[moleculeType]
id 1
label compartment_marker
color .81 .60 .21
draw-as-point 1
shape Sphere .2 1
neighborhood-size 5
coordinator 1 3
instantiate 30 random spherical surface 30 21 30 1
[/moleculeType]


[moleculeType]
id 2
label pump_in
color .11 .00 .21
shape Sphere .2
neighborhood-size 1
dynamic-neighborhood-sizing 1
coordinator 1 3
coordinator 2 7
instantiate 1 random spherical surface 30 21 30 1
[/moleculeType]

[moleculeType]
id 5
label pump_out
color .51 .50 .51
shape Sphere .2
neighborhood-size 1
dynamic-neighborhood-sizing 1
coordinator 1 3
coordinator 2 8
instantiate 1 random spherical surface 30 20 30 1
[/moleculeType]

[moleculeType]
id 4
label ligand
color .12 .12 .91
show-neighbor-lines 0
shape Sphere .2 
neighborhood-size 1
dynamic-neighborhood-sizing 1
resident-compartment-type 0
coordinator 1 7
coordinator 1 8
instantiate 6 random spherical volume 33 25 30 5
[/moleculeType]


[coordinatorType]
id 3
label membrane_section
color .92 .32 .11
opacity 0.2
geometricType plane
shape Cube 99 .02 100
isCompartment 1
neighborhood-size 20
isCreationDynamic 0
isMobile 0
isSizeDynamic 0
molecule 1 30
molecule 2 2
molecule 5 2
orientation vertex 0 1 0 pointing-at 1 0 0
instantiate 1 determined point - 30 20 30
[/coordinatorType]


[coordinatorType]
id 7
label pump_in_complex
shape Cube .2 .2 .2
molecule 4 1 0
molecule 2 1 0

[rule]
id 1
#-----------------------------------------------------------------
#load pump
#ligand will enter the compartment if it has not been there before
#note that we only test for the compartment of the receptor the 
#ligand will never become a part of this "compartment" since a 
#planar coordinator does not define a compartment
#but a barrier within a compartment that can be traversed
#-----------------------------------------------------------------
if 34.4.1.0.0.2.65
if 35.2.1.0.1.99999.3
then 34 begins-assembly
then 35 begins-assembly
parameters p 1.0
[/rule]

[rule]
id 2
#-----------------------------------------------------------------
#translocation
#change a feature state of the ligand so we know it has entered 
#the comparment
#-----------------------------------------------------------------
if 34.4.1.1
if 35.2.1.1.1.99999.3
then 34 changes-state-to 2.65
then 34 changes-colour-to 1:1:0
then 34 translocates-past-molecule 35
then 34 leaves-coordinator
parameters p 1.0
[/rule]
[/coordinatorType]


[coordinatorType]
id 8
label pump_out_complex
shape Cube .2 .2 .2
molecule 4 1 0
molecule 5 1 0
[rule]
#load pump
id 1
if 34.4.1.0.1.2.65
if 35.5.1.0.1.99999.3
then 34 begins-assembly
then 35 begins-assembly
parameters p1 0.15
[/rule]
[rule]
#translocation
id 2
if 34.4.1.1
if 35.5.1.1.1.99999.3
then 34 changes-state-to 2.0
then 34 translocates-past-molecule 35
then 34 changes-colour-to .12:.12:.91
then 34 leaves-coordinator
parameters p1 0.15
[/rule]
[/coordinatorType]


[coordinatorType]
id 10
label simulation-container
color .383 .466 .561
opacity 0.1
geometricType plane
shape Cube 100 .2 100
neighborhood-size 10
isCreationDynamic 0 
isMobile 0
#west wall
orientation vertex 0 1 0 pointing-at 1 0 0
instantiate 1 determined point  - 0 50 50
#east wall
orientation vertex 0 1 0 pointing-at -1 0 0
instantiate 1 determined point  - 100 50 50
#north wall
orientation vertex 0 1 0 pointing-at 0 0 1
instantiate 1 determined point  - 50 50 0
#south wall
orientation vertex 0 1 0 pointing-at 0 0 -1
instantiate 1 determined point  - 50 50 100
#sky wall
#ground wall
[/coordinatorType]


EOF

Example 6.5

###########
#rules.5.txt
#
#Specifying molecule rules
#This very simple example demonstrates the syntax for specifying rules
#for molecules.  The syntax is slightly different from that of rules for
#coordinators in that if lines do not begin with a tag id; instead they 
#begin with an identifier for the molecule type that they apply to. 
#
#In this example, a molecule may be created or destroyed at each time-step 
#of the simulation with some probability.
#
#See the "Making Models" section of the Magrathea manual for more details
#on the syntax of each line
# 
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]

#camera-at-from 30 20 30 14 13 30
camera-at-from 30 20 30 7 6 15

light-source 0 20 20
movie-length 40
[/simulation]

[moleculeType]
id 1
label inputSignal
color 1 0 0
shape Sphere 1
neighborhood-size 1
dynamic-neighborhood-sizing 1
[rule]
# signal creation
id 1
if 1
competitive-with 2
then 1 is-created-at-location-of 1
#parameters p1 0.00005
parameters p1 0.005
[/rule]
[rule]
# signal destruction
id 2
if 1
competitive-with 1
then 1 is-destroyed
parameters p2 0.009
[/rule]
instantiate 4 random spherical volume 10 15 10 10
[/moleculeType]



EOF

Example 6.6

###########
#rules.6.txt
#
#Specifying molecule rules
#This example builds on rules.5.txt
#In this example, a molecule may be created or destroyed at each time-step 
#of the simulation with some probability, but, before doing so, the molecule
#must be in some pre-creation or pre-destruction state.
#
#See the "Making Models" section of the Magrathea manual for more details
#on the syntax of each line
# 
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]

#camera-at-from 30 20 30 14 13 30
camera-at-from 30 20 30 7 6 15

light-source 0 20 20
movie-length 40
[/simulation]

[moleculeType]
id 1
label inputSignal
color 1 0 0
shape Sphere 1
neighborhood-size 1
dynamic-neighborhood-sizing 1

[rule]
#state change to pre-creation
id 1
if 1.1.0
competitive-with 4
then 1 changes-state-to 1.1
then 1 changes-colour-to .1:.32:.11
parameters p1 0.005
[/rule]

[rule]
#state change to pre-destruction
id 2
if 1.1.1
competitive-with 3
then 1 changes-state-to 1.0
then 1 changes-colour-to .1:.32:.11
parameters p1 0.005
[/rule]

[rule]
#creation
id 3
if 1.1.1
competitive-with 2
then 1 is-created-at-location-of 1
parameters p1 0.005
[/rule]

[rule]
#destruction
id 4
if 1.1.0
competitive-with 1
then 1 is-destroyed
parameters p2 0.009
[/rule]
instantiate 6 random spherical volume 10 15 10 10
[/moleculeType]


EOF

Example 6.7

###########
#rules.7.txt
#showing a linear coordinator used to model a microtubule or some
#other linear macromolecular structure 
#20 member molecules are moved to the line coordinator and 
#their random movement is constrained to this line
#the line coordinator is dynamically sized so it grows in length 
#as molecules join it
#the molecules have an effective radius of 2 (versus the rendered 1 unit)
#so the molecules appear spaced out along the line
#
#last tested with breve 2.6.1 and magrathea.tz 1.44
#at the time of testing, neighbor lines are only drawn if breve 2.5 is used
###########


[simulation]
camera-at-from 20 10 0 1 1 70
light-source 0 20 20
movie-length 80
[/simulation]

[moleculeType]
id 1
label line_coordinator_component_1
show-label 0
color .81 .60 .21
shape Sphere 1
draw-as-point 0
show-neighbor-lines 1
neighborhood-size 1
dynamic-neighborhood-sizing 1
feature 67 bindable-by-microtubule
feature-state 67 1 bindable-yes
feature-state 67 0 bindable-no
coordinator 1 4
coordinator 2 6
#instantiate 40 random cylindrical volume 10 15 10 0 1 0 0 105 67.1
instantiate 1 determined point - 10 15 10 - - - - - 67.1
instantiate 1 determined point - 12 15 10 - - - - - 67.1
instantiate 1 determined point - 14 15 10 - - - - - 67.1
instantiate 1 determined point - 16 15 10 - - - - - 67.1
instantiate 1 determined point - 18 15 10 - - - - - 67.1
instantiate 1 determined point - 20 15 10 - - - - - 67.1
instantiate 1 determined point - 22 15 10 - - - - - 67.1
instantiate 1 determined point - 24 15 10 - - - - - 67.1
instantiate 1 determined point - 26 15 10 - - - - - 67.1
instantiate 1 determined point - 28 15 10 - - - - - 67.1
instantiate 1 determined point - 30 15 10 - - - - - 67.1
instantiate 1 determined point - 32 15 10 - - - - - 67.1
instantiate 1 determined point - 34 15 10 - - - - - 67.1
instantiate 1 determined point - 36 15 10 - - - - - 67.1
instantiate 1 determined point - 38 15 10 - - - - - 67.1
instantiate 1 determined point - 40 15 10 - - - - - 67.1
instantiate 1 determined point - 42 15 10 - - - - - 67.1
instantiate 1 determined point - 44 15 10 - - - - - 67.1
instantiate 1 determined point - 46 15 10 - - - - - 67.1
instantiate 1 determined point - 48 15 10 - - - - - 67.1
instantiate 1 determined point - 50 15 10 - - - - - 67.1


[/moleculeType]


[moleculeType]
id 2
label motor_component
show-label 0
color .81 .80 .21
shape Sphere 1
show-neighbor-lines 1
neighborhood-size 1
dynamic-neighborhood-sizing 1
coordinator 1 5
coordinator 2 6
instantiate 1 determined point - 1 17 10 - - - - - 1.0
instantiate 1 determined point - 1 17 10 - - - - - 1.1
[/moleculeType]



[coordinatorType]
id 4
label line_coordinator
color .383 .466 .561
opacity 1
shape Cube .2 .2 .2
geometricType line
neighborhood-size 5
isCreationDynamic 0
isMobile 0
isSizeDynamic 1
molecule 1 40
orientation vertex 1 0 0 pointing-at 1 0 0
instantiate 1 determined point - 30 15 10
[/coordinatorType]


[coordinatorType]
id 5
label motor_coordinator
color .383 .466 .561
opacity 1
shape Cube 1 1 1
geometricType point
neighborhood-size 5
isCreationDynamic 1
isMobile 1
isSizeDynamic 0
molecule 2 2
instantiate 0 determined point - 30 15 10
[rule]
id 1
if 34.2.1.1.1.1.1
then 34 changes-colour-to 1:0:0
parameters p 1.0
[/rule]

[rule]
#switch binding activated
id 3
if 34.2.1.1.1.1.2
if 35.2.1.1.1.1.0
then 34 changes-state-to 1.3
then 34 changes-colour-to .81:.80:.21
then 35 changes-state-to 1.1
then 35 changes-colour-to 1:0:0
parameters p 1.0
[/rule]

[rule]
#switch binding activated
id 4
if 34.2.1.1.1.1.2
if 35.2.1.1.1.1.3
then 34 changes-state-to 1.3
then 34 changes-colour-to .81:.80:.21
then 35 changes-state-to 1.4
parameters p 1.0
[/rule]
[/coordinatorType]

[coordinatorType]
id 6
label motor_tubule
color .483 .566 .461
opacity 1
shape Cube 1 1 1
geometricType point
neighborhood-size 1
isCreationDynamic 1
isMobile 1
isSizeDynamic 0
molecule 1 1 0
molecule 2 1 0

[rule]
id 1
#begin assembly with motor
if 34.2.1.0.1.1.1
if 35.1.1.0.1.67.1
then 34 begins-assembly
then 35 begins-assembly
parameters p 1.0
[/rule]

[rule]
id 2
#signal
if 34.2.1.1.1.1.1
if 35.1.1.1.1.67.1
then 34 changes-state-to 1.2
then 35 changes-state-to 67.2
then 35 changes-colour-to 1:1:1
parameters p 1.0
[/rule]

[rule]
id 3
#leave
if 34.2.1.1.1.1.4
if 35.1.1.1.1.67.2
then 34 changes-state-to 1.1
then 34 leaves-coordinator
then 35 leaves-coordinator
parameters p 1.0
[/rule]

instantiate 0 determined point - 30 15 10
[/coordinatorType]

#****************************************************************

EOF