def loadInterfacePDB(file,name=None,native=None,wt=None):
print " Loading interface PDB %s"%(file)
if name is None:
name = name = os.path.basename(file)
if name.endswith('.pdb'):
name = name[:-4]
# Call Will's packing PDB loading function
# Note: proteins will be cartoons, cavities will be spheres
# Rosetta radii will be enabled
name = loadPackingPDB(file,name,native)
cavselname = name+"cavities"
protselname = name+"protein"
cmd.hide("lines",protselname)
backbone_colorlist = ['green', 'yellow', 'violet', 'cyan', \
'salmon', 'lime', 'slate', 'magenta', 'orange', 'marine', \
'olive', 'forest', 'firebrick', 'chocolate' ]
curr_bb_color = 0
carbon_colorlist = ['teal', 'wheat', 'grey', 'pink' ]
curr_carbon_color = 0
# Derive selections for the interface, color by chain
cmd.select("interface", "none")
cmd.select("heavy_interface", "none")
selectPolarProtons("polar_protons")
selectApolarProtons("apolar_protons")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain"+letter
cmd.select( chainname, "chain %s and not hetatm and not symbol w"%(letter) )
# Check whether any protein atoms exist with this chain ID
# JK Later, put in a special "non-interface" case for L/H antibody chains
if cmd.count_atoms("chain%s"%(letter))>0:
interfacename = "interface"+letter
cmd.select("not_this_chain", "not hetatm and not symbol w and not %s"%(chainname) )
cmd.select(interfacename, "byres %s and (not_this_chain around 4.0)"%(chainname) )
cmd.select("heavy_%s"%(interfacename), "%s and not apolar_protons"%(interfacename))
cmd.select("interface", "interface or %s"%(interfacename) )
cmd.select("heavy_interface", "heavy_interface or heavy_%s"%(interfacename) )
cmd.delete("not_this_chain")
cmd.color(backbone_colorlist[curr_bb_color], chainname)
curr_bb_color = curr_bb_color+1
if(curr_bb_color == len(backbone_colorlist)):
curr_bb_color = 0
colorCPK(interfacename,carbon_colorlist[curr_carbon_color])
curr_carbon_color = curr_carbon_color+1
if(curr_carbon_color == len(carbon_colorlist)):
curr_carbon_color = 0
cmd.color("white", "%s and polar_protons"%(interfacename))
else:
cmd.delete(chainname)
cmd.delete("apolar_protons")
cmd.delete("polar_protons")
# Show the interface in sticks, colored cpk
#cmd.hide( "cartoon", "interface" )
cmd.show( "sticks", "heavy_interface" )
cmd.zoom("interface")
cmd.show( "cartoon", "(not interface) or byres(neighbor(interface)) or byres(neighbor(byres(neighbor(interface))))" )
# Show interface waters as small purple spheres
cmd.select( "interface_water", "(symbol w or resn HOH) and (interface around 8.0)")
if cmd.count_atoms("interface_water")>0:
# Put the waters in a separate object, so that we can scale their radii
newwatername = name+"waters"
cmd.create(newwatername, "interface_water")
cmd.remove("interface_water")
cmd.color("purple", newwatername)
cmd.show( "spheres", newwatername )
#cmd.set( "sphere_scale", 0.5, newwatername )
cmd.set( "sphere_scale", 0.1, newwatername )
else:
cmd.delete("interface_water")
# Show interface ligands as pink sticks
cmd.select( "interface_hetero", "(not symbol w and not resn HOH) and (hetatm and not symbol w and not resn WSS) and (interface around 4.5)")
if cmd.count_atoms("interface_hetero")>0:
cmd.color("pink", "interface_hetero")
cmd.show( "sticks", "interface_hetero" )
else:
cmd.delete("interface_hetero")
cmd.select("none")
cmd.load( wt, "wt" )
cmd.create( "wt_A", "wt and chain A" )
cmd.create( "wt_B", "wt and chain B" )
cmd.select("none")
cmd.create( "des_A", "not wt and chain A" )
cmd.show( "surface", "des_A" )
cmd.create( "des_B", "not wt and chain B")
cmd.show( "surface", "des_B" )
cmd.align( "wt_A", "des_A" )
cmd.align( "wt_B", "des_B" )
# cmd.show( "lines", "wt_A" )
# cmd.show( "lines", "wt_B" )
cmd.set( "transparency", 1 )
cmd.zoom("interface")
return name
def loadInterfacePDB(file, name=None, native=None, wt=None):
print " Loading interface PDB %s" % (file)
if name is None:
name = name = os.path.basename(file)
if name.endswith('.pdb'):
name = name[:-4]
# Call Will's packing PDB loading function
# Note: proteins will be cartoons, cavities will be spheres
# Rosetta radii will be enabled
name = loadPackingPDB(file, name, native)
cavselname = name + "cavities"
protselname = name + "protein"
cmd.hide("lines", protselname)
backbone_colorlist = ['green', 'yellow', 'violet', 'cyan', \
'salmon', 'lime', 'slate', 'magenta', 'orange', 'marine', \
'olive', 'forest', 'firebrick', 'chocolate' ]
curr_bb_color = 0
carbon_colorlist = ['teal', 'wheat', 'grey', 'pink']
curr_carbon_color = 0
# Derive selections for the interface, color by chain
cmd.select("interface", "none")
cmd.select("heavy_interface", "none")
selectPolarProtons("polar_protons")
selectApolarProtons("apolar_protons")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain" + letter
cmd.select(chainname,
"chain %s and not hetatm and not symbol w" % (letter))
# Check whether any protein atoms exist with this chain ID
# JK Later, put in a special "non-interface" case for L/H antibody chains
if cmd.count_atoms("chain%s" % (letter)) > 0:
interfacename = "interface" + letter
cmd.select("not_this_chain",
"not hetatm and not symbol w and not %s" % (chainname))
cmd.select(
interfacename,
"byres %s and (not_this_chain around 4.0)" % (chainname))
cmd.select("heavy_%s" % (interfacename),
"%s and not apolar_protons" % (interfacename))
cmd.select("interface", "interface or %s" % (interfacename))
cmd.select("heavy_interface",
"heavy_interface or heavy_%s" % (interfacename))
cmd.delete("not_this_chain")
cmd.color(backbone_colorlist[curr_bb_color], chainname)
curr_bb_color = curr_bb_color + 1
if (curr_bb_color == len(backbone_colorlist)):
curr_bb_color = 0
colorCPK(interfacename, carbon_colorlist[curr_carbon_color])
curr_carbon_color = curr_carbon_color + 1
if (curr_carbon_color == len(carbon_colorlist)):
curr_carbon_color = 0
cmd.color("white", "%s and polar_protons" % (interfacename))
else:
cmd.delete(chainname)
cmd.delete("apolar_protons")
cmd.delete("polar_protons")
# Show the interface in sticks, colored cpk
#cmd.hide( "cartoon", "interface" )
cmd.show("sticks", "heavy_interface")
cmd.zoom("interface")
cmd.show(
"cartoon",
"(not interface) or byres(neighbor(interface)) or byres(neighbor(byres(neighbor(interface))))"
)
# Show interface waters as small purple spheres
cmd.select("interface_water",
"(symbol w or resn HOH) and (interface around 8.0)")
if cmd.count_atoms("interface_water") > 0:
# Put the waters in a separate object, so that we can scale their radii
newwatername = name + "waters"
cmd.create(newwatername, "interface_water")
cmd.remove("interface_water")
cmd.color("purple", newwatername)
cmd.show("spheres", newwatername)
#cmd.set( "sphere_scale", 0.5, newwatername )
cmd.set("sphere_scale", 0.1, newwatername)
else:
cmd.delete("interface_water")
# Show interface ligands as pink sticks
cmd.select(
"interface_hetero",
"(not symbol w and not resn HOH) and (hetatm and not symbol w and not resn WSS) and (interface around 4.5)"
)
if cmd.count_atoms("interface_hetero") > 0:
cmd.color("pink", "interface_hetero")
cmd.show("sticks", "interface_hetero")
else:
cmd.delete("interface_hetero")
cmd.select("none")
cmd.load(wt, "wt")
cmd.create("wt_A", "wt and chain A")
cmd.create("wt_B", "wt and chain B")
cmd.select("none")
cmd.create("des_A", "not wt and chain A")
cmd.show("surface", "des_A")
cmd.create("des_B", "not wt and chain B")
cmd.show("surface", "des_B")
cmd.align("wt_A", "des_A")
cmd.align("wt_B", "des_B")
# cmd.show( "lines", "wt_A" )
# cmd.show( "lines", "wt_B" )
cmd.set("transparency", 1)
cmd.zoom("interface")
return name
def stix():
backbone_colorlist = ['plutonium','wheat','green', 'yellow', 'violet', 'cyan', \
'salmon', 'lime', 'slate', 'magenta', 'orange', 'marine', \
'olive', 'forest', 'firebrick', 'chocolate' ]
curr_bb_color = 0
carbon_colorlist = ['teal', 'wheat', 'grey', 'pink' ]
curr_carbon_color = 0
# Derive selections for the interface, color by chain
cmd.select("interface", "none")
cmd.select("heavy_interface", "none")
selectPolarProtons("polar_protons")
selectApolarProtons("apolar_protons")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain"+letter
cmd.select( chainname, "chain %s and not hetatm and not symbol w"%(letter) )
# Check whether any protein atoms exist with this chain ID
# JK Later, put in a special "non-interface" case for L/H antibody chains
if cmd.count_atoms("chain%s"%(letter))>0:
interfacename = "interface"+letter
cmd.select("not_this_chain", "not hetatm and not symbol w and not %s"%(chainname) )
cmd.select(interfacename, "byres %s and (not_this_chain around 4.0)"%(chainname) )
cmd.select("heavy_%s"%(interfacename), "%s and not apolar_protons"%(interfacename))
cmd.select("interface", "interface or %s"%(interfacename) )
cmd.select("heavy_interface", "heavy_interface or heavy_%s"%(interfacename) )
cmd.delete("not_this_chain")
cmd.color(backbone_colorlist[curr_bb_color], chainname)
colorCPK(chainname,backbone_colorlist[curr_bb_color])
curr_bb_color = curr_bb_color+1
if(curr_bb_color == len(backbone_colorlist)):
curr_bb_color = 0
#colorCPK(interfacename,carbon_colorlist[curr_carbon_color])
curr_carbon_color = curr_carbon_color+1
if(curr_carbon_color == len(carbon_colorlist)):
curr_carbon_color = 0
cmd.color("white", "%s and polar_protons"%(interfacename))
else:
cmd.delete(chainname)
cmd.delete("apolar_protons")
cmd.delete("polar_protons")
# Show the interface in sticks, colored cpk
#cmd.hide( "cartoon", "interface" )
cmd.show( "sticks", "not hydro" )
cmd.zoom("interface")
cmd.show( "cartoon", "(not interface) or byres(neighbor(interface)) or byres(neighbor(byres(neighbor(interface))))" )
# Show interface waters as small purple spheres
cmd.select( "interface_water", "(symbol w or resn HOH) and (interface around 8.0)")
if cmd.count_atoms("interface_water")>0:
# Put the waters in a separate object, so that we can scale their radii
newwatername = name+"waters"
cmd.create(newwatername, "interface_water")
cmd.remove("interface_water")
cmd.color("purple", newwatername)
cmd.show( "spheres", newwatername )
cmd.set( "sphere_scale", 0.1, newwatername )
else:
cmd.delete("interface_water")
# Show interface ligands as pink sticks
cmd.select( "interface_hetero", "(not symbol w and not resn HOH) and (hetatm and not symbol w and not resn WSS) and (interface around 4.5)")
if cmd.count_atoms("interface_hetero")>0:
cmd.color("pink", "interface_hetero")
cmd.show( "sticks", "interface_hetero" )
else:
cmd.delete("interface_hetero")
# Show polar contacts
#cmd.distance("hbonds","interfaceA","interfaceB",3.2,mode=1)
cmd.distance("hbonds","interfaceA","interfaceB",4.5,mode=2)
#cmd.distance("hbonds","interfaceA","interfaceB",3.2,mode=3)
cmd.hide("labels")
cmd.hide("lines")
cmd.select("none")
def colorInterface(name="(all)"):
"""
colorInterfacePDB [<name>]
Color by chain and show interface features.
"""
cmd.hide("lines",name)
backbone_colorlist = ['green', 'yellow', 'violet', 'cyan', \
'salmon', 'lime', 'slate', 'magenta', 'orange', 'marine', \
'olive', 'forest', 'firebrick', 'chocolate' ]
curr_bb_color = 1
carbon_colorlist = ['teal', 'wheat', 'grey', 'pink' ]
curr_carbon_color = 1
# Derive selections for the interface, color by chain
cmd.select("interface", "none")
cmd.select("heavy_interface", "none")
selectPolarProtons("polar_protons")
selectApolarProtons("apolar_protons")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain"+letter
cmd.select( chainname, "chain %s and not hetatm and not symbol w and %s" % (letter, name) )
# Check whether any protein atoms exist with this chain ID
# JK Later, put in a special "non-interface" case for L/H antibody chains
if cmd.count_atoms("chain%s"%(letter))>0:
interfacename = "interface"+letter
cmd.select("not_this_chain", "not hetatm and not symbol w and not %s and %s" % (chainname, name) )
cmd.select(interfacename, "byres %s and (not_this_chain around 6.0)"%(chainname) )
cmd.select("heavy_%s"%(interfacename), "%s and not apolar_protons"%(interfacename))
cmd.select("interface", "interface or %s"%(interfacename) )
cmd.select("heavy_interface", "heavy_interface or heavy_%s"%(interfacename) )
cmd.delete("not_this_chain")
cmd.color(backbone_colorlist[curr_bb_color], chainname)
colorCPK(interfacename,backbone_colorlist[curr_bb_color])
curr_bb_color = curr_bb_color+1
if(curr_bb_color == len(backbone_colorlist)):
curr_bb_color = 0
curr_carbon_color = curr_carbon_color+1
if(curr_carbon_color == len(carbon_colorlist)):
curr_carbon_color = 0
cmd.color("white", "%s and polar_protons"%(interfacename))
else:
cmd.delete(chainname)
cmd.delete("apolar_protons")
cmd.delete("polar_protons")
# Show the interface in sticks, colored cpk
# cmd.hide( "cartoon", "interface" )
cmd.show( "sticks", "heavy_interface" )
#cmd.show( "cartoon", "(not interface) or byres(neighbor(interface)) or byres(neighbor(byres(neighbor(interface))))" )
cmd.show( "cartoon", name )
# Show interface waters as small purple spheres
cmd.select( "interface_water", "(symbol w or resn HOH) and (interface around 8.0)")
if cmd.count_atoms("interface_water")>0:
# Put the waters in a separate object, so that we can scale their radii
newwatername = name+"waters"
cmd.create(newwatername, "interface_water")
cmd.remove("interface_water")
cmd.color("purple", newwatername)
cmd.show( "spheres", newwatername )
cmd.set( "sphere_scale", 0.1, newwatername )
else:
cmd.delete("interface_water")
# Show interface ligands as pink sticks
cmd.select( "interface_hetero", "(not symbol w and not resn HOH) and (hetatm and not symbol w and not resn WSS) and (interface around 4.5)")
if cmd.count_atoms("interface_hetero")>0:
cmd.color("pink", "interface_hetero")
cmd.show( "sticks", "interface_hetero" )
else:
cmd.delete("interface_hetero")
cmd.set( "transparency", 1 )
cmd.zoom("interface")
return name
def surfaceInterfacePDB():
cmd.hide("lines")
backbone_colorlist = [ 'forest','gold', 'violet', 'cyan', \
'salmon', 'lime', 'slate', 'magenta', 'orange', 'marine', \
'olive', 'forest', 'firebrick', 'chocolate' ]
curr_bb_color = 0
carbon_colorlist = ['titanium', 'wheat', 'grey', 'pink' ]
curr_carbon_color = 0
# Derive selections for the interface, color by chain
cmd.select("interface", "none")
cmd.select("heavy_interface", "none")
selectPolarProtons("polar_protons")
selectApolarProtons("apolar_protons")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain"+letter
cmd.select( chainname, "chain %s and not hetatm and not symbol w"%(letter) )
# Check whether any protein atoms exist with this chain ID
# JK Later, put in a special "non-interface" case for L/H antibody chains
if cmd.count_atoms("chain%s"%(letter))>0:
interfacename = "interface"+letter
cmd.select("not_this_chain", "not hetatm and not symbol w and not %s"%(chainname) )
cmd.select(interfacename, "byres %s and (not_this_chain around 4.0)"%(chainname) )
cmd.select("heavy_%s"%(interfacename), "%s and not apolar_protons"%(interfacename))
cmd.select("interface", "interface or %s"%(interfacename) )
cmd.select("heavy_interface", "heavy_interface or heavy_%s"%(interfacename) )
cmd.delete("not_this_chain")
cmd.color(backbone_colorlist[curr_bb_color], chainname)
#changing....
colorCPK(interfacename,backbone_colorlist[curr_bb_color])
curr_bb_color = curr_bb_color+1
if(curr_bb_color == len(backbone_colorlist)):
curr_bb_color = 0
#colorCPK(interfacename,carbon_colorlist[curr_carbon_color])
curr_carbon_color = curr_carbon_color+1
if(curr_carbon_color == len(carbon_colorlist)):
curr_carbon_color = 0
cmd.color("white", "%s and polar_protons"%(interfacename))
else:
cmd.delete(chainname)
cmd.delete("apolar_protons")
cmd.delete("polar_protons")
# Show the interface in sticks, colored cpk
#cmd.hide( "cartoon", "interface" )
cmd.show( "sticks", "heavy_interface" )
cmd.create("design", "chain B")
cmd.create("target", "chain A")
cmd.show( "surface", "target" )
cmd.show( "surface", "design" )
cmd.set( "transparency", 0 )
cmd.show( "cartoon", "(not interface) or byres(neighbor(interface)) or byres(neighbor(byres(neighbor(interface))))" )
# Show interface waters as small purple spheres
cmd.select( "interface_water", "(symbol w or resn HOH) and (interface around 8.0)")
if cmd.count_atoms("interface_water")>0:
# Put the waters in a separate object, so that we can scale their radii
newwatername = name+"waters"
cmd.create(newwatername, "interface_water")
cmd.remove("interface_water")
cmd.color("purple", newwatername)
cmd.show( "spheres", newwatername )
cmd.set( "sphere_scale", 0.1, newwatername )
else:
cmd.delete("interface_water")
# Show interface ligands as pink sticks
cmd.select( "interface_hetero", "(not symbol w and not resn HOH) and (hetatm and not symbol w and not resn WSS) and (interface around 4.5)")
if cmd.count_atoms("interface_hetero")>0:
cmd.color("pink", "interface_hetero")
cmd.show( "sticks", "interface_hetero" )
else:
cmd.delete("interface_hetero")
# Show polar contacts
cmd.distance("hbonds","interfaceA","interfaceB",3.2,mode=2)
cmd.hide("labels")
# Show vacuum electrostatics
cmd.util.protein_vacuum_esp("design", mode=2, quiet=0)
cmd.util.protein_vacuum_esp("target", mode=2, quiet=0)
cmd.disable("design_e_chg")
cmd.disable("design_e_map")
cmd.disable("design_e_pot")
cmd.disable("target_e_chg")
cmd.disable("target_e_map")
cmd.disable("target_e_pot")
cmd.disable("design")
cmd.disable("target")
cmd.zoom("interface")
cmd.remove("sele")
cmd.select("none")