Appendix F
# Another example pddf ... this time of a sea of viral coat proteins
#
# again, this is not meant to be an accurate simulation, but is a demonstration
# file. (Haven't worked out all the links yet!)
#
# This is the hexon that binds directly to the penton
#
Model HexonP
{
Sphere hexon_center 1 <0,0,0> lightgreen
#site name twist
site Aside <1,0,0> <1,0,0> <0,0,1>
site Bside <0.5,0.809017,-0.309017> <0.5,0.809017,-0.309017> <0.16246,0.262866,0.951056>
site Cside <-0.5,0.809017,-0.309017> <-0.5,0.809017,-0.309017> <-0.16246,0.262866,0.951056>
site Dside <-1,0,0> <-1,0,0> <0,0,1>
site Eside <-0.5,-0.809017,-0.309017> <-0.5,-0.809017,-0.309017> <-0.16246,-0.262866,0.951056>
site Fside <0.5,-0.809017,-0.309017> <0.5,-0.809017,-0.309017> <0.16246,-0.262866,0.951056>
State unbound
State bound # a new state, with no physical changes
colour hexon_center = green
# The event list is all of the form:
# Event: link { A B } | break | random (chance / cycle)
# StateA -> StateB
Event bind { } unbound -> bound
Event break { all } bound -> unbound
}
#
# This is the edge hexon that binds to hexonP, and forms the exact
# center of an edge
#
Model HexonE
{
Sphere hexon_center 1 <0,0,0> lightblue
#site name twist
site Aside <1,0,0> <1,0,0> <0,0,1>
site Bside <0.5,0.809017,-0.309017> <0.5,0.809017,-0.309017> <0.16246,0.262866,0.951056>
site Cside <-0.5,0.809017,-0.309017> <-0.5,0.809017,-0.309017> <-0.16246,0.262866,0.951056>
site Dside <-1,0,0> <-1,0,0> <0,0,1>
site Eside <-0.5,-0.809017,-0.309017> <-0.5,-0.809017,-0.309017> <-0.16246,-0.262866,0.951056>
site Fside <0.5,-0.809017,-0.309017> <0.5,-0.809017,-0.309017> <0.16246,-0.262866,0.951056>
State unbound
State bound # a new state, with no physical changes
colour hexon_center = blue
# The event list is all of the form:
# Event: link { A B } | break | random (chance / cycle)
# StateA -> StateB
Event bind { } unbound -> bound
Event break { all } bound -> unbound
}
#
# This is the "face" hexon; three of these make up the center of each
# icosahedron face.
#
Model HexonC
{
Sphere hexon_center 1 <0,0,0> gray
#site name twist
site Aside <1,0,0> <1,0,0> <0,0,1>
site Bside <0.5,0.866025,0> <0.5,0.866025,0> <0,0,1>
site Cside <-0.5,0.866025,0> <-0.5,0.866025,0> <0,0,1>
site Dside <-1,0,0> <-1,0,0> <0,0,1>
site Eside <-0.5,-0.866025,0> <-0.5,-0.866025,0> <0,0,1>
site Fside <0.5,-0.866025,0> <0.5,-0.866025,0> <0,0,1>
State unbound
State bound # a new state, with no physical changes
colour hexon_center = black
# The event list is all of the form:
# Event: link { A B } | break | random (chance / cycle)
# StateA -> StateB
Event bind { } unbound -> bound
Event break { all } bound -> unbound
}
Model Penton
{
Sphere penton_center 0.9 <0,0,0> pink
#site name twist
site Aside <0.85065081,0,-0.5257311> <0.85065081,0,-0.5257311> <0.5257311,0,0.85065081>
site Bside <0.26286556,0.809017,-0.5257311> <0.26286556,0.809017,-0.5257311> <0.16245985,0.5,0.85065081>
site Cside <-0.68819096,0.5,-0.5257311> <-0.68819096,0.5,-0.5257311> <-0.42532539,0.309017,0.85065081>
site Dside <-0.68819096,-0.5,-0.5257311> <-0.68819096,-0.5,-0.5257311> <-0.42532539,-0.309017,0.85065081>
site Eside <0.26286556,-0.809017,-0.5257311> <0.26286556,-0.809017,-0.5257311> <0.16245985,-0.5,0.85065081>
State unbound
State bound # a new state, with no physical changes
colour penton_center = red
State bloopy
colour penton_center = black;
# The event list is all of the form:
# Event: link { A B } | break | random (chance / cycle)
# StateA -> StateB
Event bind { } unbound -> bound
Event break { all } bound -> unbound
}
# specify links and states, and give their binding and breaking chance
# links are transitive.
Binding Penton Aside unbound to HexonP Aside unbound = 0.0001 0
Binding Penton Bside unbound to HexonP Aside unbound = 0.0001 0
Binding Penton Cside unbound to HexonP Aside unbound = 0.0001 0
Binding Penton Dside unbound to HexonP Aside unbound = 0.0001 0
Binding Penton Eside unbound to HexonP Aside unbound = 0.0001 0
#Binding HexonP Dside unbound to HexonE Aside unbound = 0.0001 0
#Binding HexonP Dside unbound to HexonE Dside unbound = 0.0001 0
#Binding HexonP Bside unbound to HexonP Fside unbound = 0.0001 0
#Binding HexonP Fside unbound to HexonP Bside unbound = 0.0001 0
#---------------
Binding Penton Aside bound to HexonP Aside unbound = 0.9 0
Binding Penton Bside bound to HexonP Aside unbound = 0.9 0
Binding Penton Cside bound to HexonP Aside unbound = 0.9 0
Binding Penton Dside bound to HexonP Aside unbound = 0.9 0
Binding Penton Eside bound to HexonP Aside unbound = 0.9 0
Binding HexonP Dside bound to HexonE Aside unbound = 0.9 0
Binding HexonP Dside bound to HexonE Dside unbound = 0.9 0
#Binding HexonP Bside bound to HexonP Fside unbound = 0.9 0
#Binding HexonP Fside bound to HexonP Bside unbound = 0.9 0
Binding HexonP Eside bound to HexonC Fside unbound = 0.9 0
#Binding HexonP Cside bound to HexonC Eside unbound = 0.9 0
#Binding HexonC Bside bound to HexonC Cside unbound = 0.9 0
#Binding HexonC Cside bound to HexonC Bside unbound = 0.9 0
#Binding HexonC Aside bound to HexonE Fside unbound = 0.9 0
#Binding HexonC Aside bound to HexonC Cside unbound = 0.9 0
#Binding HexonC Dside bound to HexonE Bside unbound = 0.9 0
#Binding HexonC Dside bound to HexonC Eside unbound = 0.9 0
#---------------
Binding Penton Aside unbound to HexonP Aside bound = 0.9 0
Binding Penton Bside unbound to HexonP Aside bound = 0.9 0
Binding Penton Cside unbound to HexonP Aside bound = 0.9 0
Binding Penton Dside unbound to HexonP Aside bound = 0.9 0
Binding Penton Eside unbound to HexonP Aside bound = 0.9 0
Binding HexonP Dside unbound to HexonE Aside bound = 0.9 0
Binding HexonP Dside unbound to HexonE Dside bound = 0.9 0
#Binding HexonP Bside unbound to HexonP Fside bound = 0.9 0
#Binding HexonP Fside unbound to HexonP Bside bound = 0.9 0
Binding HexonP Eside unbound to HexonC Fside bound = 0.9 0
#Binding HexonP Cside unbound to HexonC Eside bound = 0.9 0
#Binding HexonC Bside unbound to HexonC Cside bound = 0.9 0
#Binding HexonC Cside unbound to HexonC Bside bound = 0.9 0
#Binding HexonC Aside unbound to HexonE Fside bound = 0.9 0
#Binding HexonC Aside unbound to HexonC Cside bound = 0.9 0
#Binding HexonC Dside unbound to HexonE Bside bound = 0.9 0
#Binding HexonC Dside unbound to HexonC Eside bound = 0.9 0
#---------------
Binding Penton Aside bound to HexonP Aside bound = 1 0
Binding Penton Bside bound to HexonP Aside bound = 1 0
Binding Penton Cside bound to HexonP Aside bound = 1 0
Binding Penton Dside bound to HexonP Aside bound = 1 0
Binding Penton Eside bound to HexonP Aside bound = 1 0
Binding HexonP Dside bound to HexonE Aside bound = 1 0
Binding HexonP Dside bound to HexonE Dside bound = 1 0
Binding HexonP Bside bound to HexonP Fside bound = 1 0
Binding HexonP Fside bound to HexonP Bside bound = 1 0
Binding HexonP Eside bound to HexonC Fside bound = 1 0
#Binding HexonP Cside bound to HexonC Eside bound = 1 0
#Binding HexonC Bside bound to HexonC Cside bound = 1 0
#Binding HexonC Cside bound to HexonC Bside bound = 1 0
#Binding HexonC Aside bound to HexonE Fside bound = 1 0
#Binding HexonC Aside bound to HexonC Cside bound = 1 0
#Binding HexonC Dside bound to HexonE Bside bound = 1 0
#Binding HexonC Dside bound to HexonC Eside bound = 1 0
# Aside generic bind
#Binding Antibody all to Dimer top all = 1 0
# some environment constants
Temperature 310 # kelvin - physiological temperature
Viscosity 0.62 # approximate viscosity for water at 37 degrees Celsius
TimeScale 100 # 100 nanoseconds per program cycle
# Finally, specify the mix of molecules in solution.
#Mix Dimer 90% Antibody 10%
Mix Penton 8% HexonP 37% HexonE 18% H