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