Difference between revisions of "Example model files for Magrathea"

From irefindex
(New page: Copy and paste this file to model.txt and move to the same directory as magrathea.tz to run. == Example 1. Point coordinator representing an interaction == <pre> ########### #interacti...)
 
Line 52: Line 52:
 
molecule 1 1
 
molecule 1 1
 
molecule 2 1
 
molecule 2 1
 +
[/coordinatorType]
 +
 +
#****************************************************************
 +
 +
EOF
 +
 +
</pre>
 +
 +
== Example 2. Point coordinator representing a complex ==
 +
 +
<pre>
 +
 +
###########
 +
#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
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###########
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 +
 +
[simulation]
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camera-at-from 10 10 0 0 1 30
 +
light-source 0 20 20
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movie-length 10
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[/simulation]
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 +
[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]
 
[/coordinatorType]
  

Revision as of 17:07, 4 March 2009

Copy and paste this file to 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
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