Difference between revisions of "Example model files for Magrathea"
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Revision as of 17:09, 5 March 2009
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
- 1 Example 1. Point coordinator representing an interaction
- 2 Example 2. Point coordinator representing a complex
- 3 Example 3. Point coordinator representing a compartment
- 4 Example 4. Plane coordinator representing a membrane section.
- 5 Example 5. Line coordinator representing a microtubule.
- 6 Example 6. Coordinators and rules.
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.
########### #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
########### #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