Example model files for Magrathea
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Revision as of 19:08, 4 March 2009 by Ian.donaldson (talk | contribs)
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.
Contents
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
