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