def na():
cmd.view('v', 'store')
object = cmd.get_names()[0]
if object[0] == 'd':
pdbid = object[1:5]
chainid = object[5:6]
else:
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na", "%s and chain %s and not hydro" % (object, "B"))
cmd.select("native_na", "%s and chain %s and not hydro" % (pdbid, chainid))
cmd.select("other_na", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("native_na", "design_na")
cmd.hide("lines", "all")
cmd.show("sticks", "native_na")
cmd.show("cartoon", "native_na")
cmd.select("none")
cmd.orient(object)
pdbid = pdbid.lower()
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
def nat(pdbid, chainid):
cmd.view('v', 'store')
object = cmd.get_names()[0]
cmd.fetch(pdbid)
cmd.select("design_nat", "%s and chain %s and not hydro" % (object, "B"))
cmd.select("native_nat",
"%s and chain %s and not hydro" % (pdbid, chainid))
cmd.select("other_nat", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("design_nat", "native_nat")
cmd.select("none")
cmd.orient(object)
cmd.hide("lines", "all")
cmd.show("sticks", "native_nat")
cmd.show("cartoon", "native_nat")
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
def nat(pdbid,chainid):
cmd.view('v', 'store');
object = cmd.get_names()[0]
cmd.fetch(pdbid)
cmd.select("design_nat","%s and chain %s and not hydro"%(object,"B"))
cmd.select("native_nat","%s and chain %s and not hydro"%(pdbid,chainid))
cmd.select("other_nat","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("design_nat","native_nat")
cmd.select("none")
cmd.orient(object)
cmd.hide("lines","all");
cmd.show("sticks","native_nat");
cmd.show("cartoon","native_nat");
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
def na():
cmd.view('v', 'store');
object = cmd.get_names()[0]
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na","%s and chain %s"%(object,"B"))
cmd.select("native_na","%s and chain %s"%(pdbid,chainid))
cmd.select("other_na","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("design_na","native_na")
cmd.select("none")
cmd.orient(object)
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
def na():
cmd.view('v', 'store');
object = cmd.get_names()[0]
if object[0] == 'd':
pdbid = object[1:5]
chainid = object[5:6]
else:
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na","%s and chain %s and not hydro"%(object,"B"))
cmd.select("native_na","%s and chain %s and not hydro"%(pdbid,chainid))
cmd.select("other_na","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("native_na","design_na")
cmd.hide("lines","all");
cmd.show("sticks","native_na");
cmd.show("cartoon","native_na");
cmd.select("none")
cmd.orient(object)
pdbid = pdbid.lower()
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
def na():
cmd.view('v', 'store')
object = cmd.get_names()[0]
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na", "%s and chain %s" % (object, "B"))
cmd.select("native_na", "%s and chain %s" % (pdbid, chainid))
cmd.select("other_na", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("design_na", "native_na")
cmd.select("none")
cmd.orient(object)
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
def info():
object = cmd.get_names()[0]
if object[0] == 'd':
pdbid = object[1:5]
chainid = object[5:6]
else:
pdbid = object[0:4]
chainid = object[4:5]
pdbid = pdbid.lower()
cmd.system("open http://pdb.org/pdb/explore/explore.do?structureId=%s"%(pdbid))
def info():
object = cmd.get_names()[0]
if object[0] == 'd':
pdbid = object[1:5]
chainid = object[5:6]
else:
pdbid = object[0:4]
chainid = object[4:5]
pdbid = pdbid.lower()
cmd.system("open http://pdb.org/pdb/explore/explore.do?structureId=%s" %
(pdbid))
#index = sys.argv.index("--")
#params = sys.argv[index:]
#if(len(params) == 2):
#path = params[1]
#cmd.cd(path)
#else:
#print "No Path specified"
except ValueError:
print "No Path specified"
for file in glob("*.pdb"):
print "file: ", file
listname = file.split(".")
name = listname[0]
cmd.load(file, name)
cmd.system("mv " + file + " ../pdb/")
cmd.hide("all")
cmd.show("sticks")
cmd.reset()
cmd.origin(position=[0.0, 0.0, 0.0])
cmd.save(name + "stix.wrl")
cmd.hide("all")
cmd.show("ribbon")
cmd.reset()
cmd.origin(position=[0.0, 0.0, 0.0])
cmd.save(name + "rib.wrl")
cmd.hide("all")
preset.pretty(name)
cmd.reset()
cmd.origin(position=[0.0, 0.0, 0.0])
cmd.save(name + "cart.wrl")
#index = sys.argv.index("--")
#params = sys.argv[index:]
#if(len(params) == 2):
#path = params[1]
#cmd.cd(path)
#else:
#print "No Path specified"
except ValueError:
print "No Path specified"
for file in glob("*.pdb"):
print "file: ", file
listname = file.split(".")
name = listname[0];
cmd.load(file, name)
cmd.system("mv " + file + " ../pdb/")
cmd.hide("all")
cmd.show("sticks")
cmd.reset()
cmd.origin(position=[0.0,0.0,0.0])
cmd.save(name + "stix.wrl")
cmd.hide("all")
cmd.show("ribbon")
cmd.reset()
cmd.origin(position=[0.0,0.0,0.0])
cmd.save(name + "rib.wrl")
cmd.hide("all")
preset.pretty(name)
cmd.reset()
cmd.origin(position=[0.0,0.0,0.0])
cmd.save(name + "cart.wrl")