def fatslim_apl_prot():
global REF_BEAD
setup()
FILENAME = BILAYER_PROT
REF_BEAD = BILAYER_PROT_REF
# Load file
cmd.load("%s.pdb" % FILENAME)
main_obj = "%s" % FILENAME
cmd.disable(main_obj)
traj = load_trajectory("%s.gro" % FILENAME, "%s.ndx" % FILENAME)
traj.initialize()
frame = traj[0]
draw_pbc_box(main_obj)
cmd.create("protein", "resi 1-160")
cmd.hide("lines", "protein")
cmd.color("yellow", "protein")
cmd.show("cartoon", "protein")
cmd.show("surface", "protein")
cmd.set("transparency", 0.5, "protein")
cmd.set("surface_color", "yelloworange", "protein")
# Show leaflets
show_leaflets(frame)
# Show stuff related to APL
show_apl(frame)
print("Bilayer with protein loaded!")
def fatslim_apl_prot():
global REF_BEAD
setup()
FILENAME = BILAYER_PROT
REF_BEAD = BILAYER_PROT_REF
# Load file
cmd.load("%s.pdb" % FILENAME)
main_obj = "%s" % FILENAME
cmd.disable(main_obj)
traj = load_trajectory("%s.gro" % FILENAME, "%s.ndx" % FILENAME)
traj.initialize()
frame = traj[0]
draw_pbc_box(main_obj)
cmd.create("protein", "resi 1-160")
cmd.hide("lines", "protein")
cmd.color("yellow", "protein")
cmd.show("cartoon", "protein")
cmd.show("surface", "protein")
cmd.set("transparency", 0.5, "protein")
cmd.set("surface_color", "yelloworange", "protein")
# Show leaflets
show_leaflets(frame)
# Show stuff related to APL
show_apl(frame)
print("Bilayer with protein loaded!")
def fatslim_bilayer():
global REF_BEAD
REF_BEAD = BILAYER_REF
setup()
# Load file
cmd.load("%s.pdb" % BILAYER)
main_obj = "bilayer"
cmd.disable(main_obj)
traj = load_trajectory("%s.gro" % BILAYER, "%s.ndx" % BILAYER)
traj.initialize()
frame = traj[0]
draw_pbc_box(main_obj)
print("Bilayer Loaded!")
# Show lipids
cmd.create("lipids", "resname DMPC")
cmd.hide("lines", "lipids")
cmd.show("spheres", "lipids")
# Show water
cmd.create("water", "resname SOL")
cmd.hide("lines", "water")
cmd.set("solvent_radius", 2)
cmd.show("surface", "water")
cmd.color("skyblue", "water")
cmd.set("transparency", 0.5, "water")
# cmd.rebuild()
# cmd.refresh()
# Show positions
show_positions(frame)
# Show directions
show_directions(frame)
# Show ref bead and its neighbors
show_ref(frame)
show_ref_ns(frame)
# Show normals
show_normals(frame)
# Identify leaflets
show_leaflets(frame)
# Calculate and show normals
show_leaflet_normals(frame)
# Show stuff related to thickness
show_thickness(frame)
# Show stuff related to APL
show_apl(frame)
# Zoom on leaflets
cmd.zoom("all", 5)
def fatslim_bilayer():
global REF_BEAD
REF_BEAD = BILAYER_REF
setup()
# Load file
cmd.load("%s.pdb" % BILAYER)
main_obj = "bilayer"
cmd.disable(main_obj)
traj = load_trajectory("%s.gro" % BILAYER, "%s.ndx" % BILAYER)
traj.initialize()
frame = traj[0]
draw_pbc_box(main_obj)
print("Bilayer Loaded!")
# Show lipids
cmd.create("lipids", "resname DMPC")
cmd.hide("lines", "lipids")
cmd.show("spheres", "lipids")
# Show water
cmd.create("water", "resname SOL")
cmd.hide("lines", "water")
cmd.set("solvent_radius", 2)
cmd.show("surface", "water")
cmd.color("skyblue", "water")
cmd.set("transparency", 0.5, "water")
# cmd.rebuild()
# cmd.refresh()
# Show positions
show_positions(frame)
# Show directions
show_directions(frame)
# Show ref bead and its neighbors
show_ref(frame)
show_ref_ns(frame)
# Show normals
show_normals(frame)
# Identify leaflets
show_leaflets(frame)
# Calculate and show normals
show_leaflet_normals(frame)
# Show stuff related to thickness
show_thickness(frame)
# Show stuff related to APL
show_apl(frame)
# Zoom on leaflets
cmd.zoom("all", 5)
def fatslim_vesicle():
setup()
global REF_BEAD
REF_BEAD = VESICLE_REF
# Load file
cmd.load("%s.pdb" % VESICLE)
main_obj = "vesicle"
cmd.disable(main_obj)
traj = load_trajectory("%s.gro" % VESICLE, "%s.ndx" % VESICLE)
traj.initialize()
frame = traj[0]
draw_pbc_box(main_obj)
print("Vesicle Loaded!")
# Show positions
show_positions(frame)
# Show directions
show_directions(frame)
# Show ref bead and its neighbors
show_ref(frame)
show_ref_ns(frame)
# Show normals
show_normals(frame)
# Identify leaflets
show_leaflets(frame)
# Calculate and show normals
show_leaflet_normals(frame)
# Show stuff related to thickness
show_thickness(frame)
# Show stuff related to APL
show_apl(frame)
def fatslim_vesicle():
setup()
global REF_BEAD
REF_BEAD = VESICLE_REF
# Load file
cmd.load("%s.pdb" % VESICLE)
main_obj = "vesicle"
cmd.disable(main_obj)
traj = load_trajectory("%s.gro" % VESICLE, "%s.ndx" % VESICLE)
traj.initialize()
frame = traj[0]
draw_pbc_box(main_obj)
print("Vesicle Loaded!")
# Show positions
show_positions(frame)
# Show directions
show_directions(frame)
# Show ref bead and its neighbors
show_ref(frame)
show_ref_ns(frame)
# Show normals
show_normals(frame)
# Identify leaflets
show_leaflets(frame)
# Calculate and show normals
show_leaflet_normals(frame)
# Show stuff related to thickness
show_thickness(frame)
# Show stuff related to APL
show_apl(frame)