def ligand_sites(selection="(all)",_self=cmd):
cmd=_self
try:
s = tmp_sele
cmd.select(s,selection)
polar_contacts = _get_polar_contacts_name(s,_self)
_prepare(s,polar_contacts,_self=cmd)
host = "_preset_host"
solvent = "_preset_solvent"
near_solvent = "_preset_solvent"
lig = "_preset_lig"
cmd.select(host,s+" and "+prot_and_dna_sele)
cmd.select(solvent,s+" and "+solv_sele)
cmd.select(lig,s+" and "+lig_sele)
cmd.select(near_solvent,s+" and ("+solvent+" within 4 of "+lig+")")
cmd.flag("ignore",host,"clear")
cmd.flag("ignore",lig+"|"+solvent,"set")
util.chainbow(host,_self=cmd)
util.cbc(lig,_self=cmd)
util.cbac("(("+s+") and not elem c)",_self=cmd)
cmd.hide("everything",s)
cmd.show("ribbon",host)
cmd.show("lines","("+s+" and byres ("+host+" within 5 of "+lig+"))")
cmd.show("surface","("+s+" and ((rep lines expand 4) within 6 of "+lig+"))")
cmd.set("two_sided_lighting",1) # global setting
cmd.set("transparency",0,s)
cmd.set("surface_quality",0,s)
cmd.show("sticks",lig)
cmd.show("sticks",solvent+" and neighbor "+lig)
cmd.show("lines","("+s+" and (rep lines extend 1) and "+lig+")")
if cmd.count_atoms(lig):
cmd.dist(polar_contacts,host+"|"+near_solvent,lig+"|"+near_solvent,mode=2,quiet=1,label=0,reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.hide("labels",polar_contacts)
cmd.show("dashes",polar_contacts)
else:
cmd.delete(polar_contacts)
cmd.show("nb_spheres",lig+"|"+host+"|"+near_solvent)
if cmd.count_atoms(lig):
cmd.zoom(lig,3)
cmd.delete(host)
cmd.delete(solvent)
cmd.delete(near_solvent)
cmd.delete(lig)
except:
traceback.print_exc()
cmd.delete(s)
def protein_assign_charges_and_radii(obj_name,_self=cmd):
pymol=_self._pymol
cmd=_self
from chempy.champ import assign
# apply a few kludges
# convent Seleno-methionine to methionine
cmd.alter(obj_name+"///MSE/SE","elem='S';name='SD'",quiet=1)
cmd.alter(obj_name+"///MSE/","resn='MET'",quiet=1)
cmd.flag("ignore",obj_name,"clear")
# remove alternate conformers
cmd.remove(obj_name+" and not alt ''+A")
cmd.alter(obj_name,"alt=''")
cmd.sort(obj_name)
cmd.fix_chemistry(obj_name,obj_name,1)
# make sure all atoms are included...
cmd.alter(obj_name,"q=1.0",quiet=1)
print " Util: Fixing termini and assigning formal charges..."
assign.missing_c_termini(obj_name,quiet=1,_self=_self)
while not assign.formal_charges(obj_name,quiet=1,_self=_self):
print " WARNING: unrecognized or incomplete residues are being deleted:"
cmd.iterate("(byres ("+obj_name+" and flag 23)) and flag 31",
'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"',quiet=1)
cmd.remove("byres ("+obj_name+" and flag 23)") # get rid of residues that weren't assigned
assign.missing_c_termini(obj_name,quiet=1,_self=_self)
print " Util: Assigning Amber 99 charges and radii..."
cmd.h_add(obj_name)
if not assign.amber99(obj_name,quiet=1,_self=_self):
print " WARNING: some unassigned atoms are being deleted:"
cmd.iterate("byres ("+obj_name+" and flag 23)",
'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"+name+"? ["+elem+"]"',quiet=1)
cmd.remove(obj_name+" and flag 23") # get rid of any atoms that weren't assigned
# show the user what the net charges are...
formal = sum_formal_charges(obj_name,quiet=0,_self=_self)
partial = sum_partial_charges(obj_name,quiet=0,_self=_self)
if round(formal)!=round(partial):
print " WARNING: formal and partial charge sums don't match -- there is a problem!"
def ligand_sites(selection="(all)", _self=cmd):
cmd = _self
try:
s = tmp_sele
cmd.select(s, selection)
polar_contacts = _get_polar_contacts_name(s, _self)
_prepare(s, polar_contacts, _self=cmd)
host = "_preset_host"
solvent = "_preset_solvent"
near_solvent = "_preset_solvent"
lig = "_preset_lig"
cmd.select(host, s + " and " + prot_and_dna_sele)
cmd.select(solvent, s + " and " + solv_sele)
cmd.select(lig, s + " and " + lig_sele)
cmd.select(near_solvent,
s + " and (" + solvent + " within 4 of " + lig + ")")
cmd.flag("ignore", host, "clear")
cmd.flag("ignore", lig + "|" + solvent, "set")
util.chainbow(host, _self=cmd)
util.cbc(lig, _self=cmd)
util.cbac("((" + s + ") and not elem c)", _self=cmd)
cmd.hide("everything", s)
cmd.show("ribbon", host)
cmd.show(
"lines",
"(" + s + " and byres (" + host + " within 5 of " + lig + "))")
cmd.show(
"surface",
"(" + s + " and ((rep lines expand 4) within 6 of " + lig + "))")
cmd.set("two_sided_lighting", 1) # global setting
cmd.set("transparency", 0, s)
cmd.set("surface_quality", 0, s)
cmd.show("sticks", lig)
cmd.show("sticks", solvent + " and neighbor " + lig)
cmd.show("lines",
"(" + s + " and (rep lines extend 1) and " + lig + ")")
if cmd.count_atoms(lig):
cmd.dist(polar_contacts,
host + "|" + near_solvent,
lig + "|" + near_solvent,
mode=2,
quiet=1,
label=0,
reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.hide("labels", polar_contacts)
cmd.show("dashes", polar_contacts)
else:
cmd.delete(polar_contacts)
cmd.show("nb_spheres", lig + "|" + host + "|" + near_solvent)
if cmd.count_atoms(lig):
cmd.zoom(lig, 3)
cmd.delete(host)
cmd.delete(solvent)
cmd.delete(near_solvent)
cmd.delete(lig)
except:
traceback.print_exc()
