Пример #1
0
def simple(selection="(all)", _self=cmd):
    cmd = _self
    s = tmp_sele
    cmd.select(s, selection)
    _prepare(s, _self=cmd)
    util.cbc(s, _self=cmd)
    cmd.show("ribbon", s)
    cmd.show(
        "lines", "(byres ((" + s + " & r. CYS+CYX & n. SG) & bound_to (" + s +
        " & r. CYS+CYX & n. SG))) & n. CA+CB+SG")
    # try to show what covalent ligands are connected to...
    cmd.show("sticks", "(" + lig_sele + " and (" + s + ")) extend 2")
    cmd.show(
        "sticks", "byres ((" + lig_sele + " and (" + s +
        ") and not resn ACE+NAC+NME+NH2) extend 1)")
    cmd.hide("sticks", "(" + s + ") and ((not rep sticks) extend 1)")
    cmd.show("sticks", "(" + lig_sele + " and (" + s + ")) extend 2")
    # color by atom if lines or sticks are shown
    util.cnc("(( rep lines or rep sticks or (" + lig_and_solv_sele +
             ")) and (" + s + "))",
             _self=cmd)
    cmd.show("nonbonded", "(" + lig_and_solv_sele + " and (" + s + "))")
    cmd.show("lines", "(" + lig_and_solv_sele + " and (" + s + "))")
    if cmd.count_atoms(s):
        cmd.zoom(s)
    cmd.delete(s)
Пример #2
0
def pretty_solv(selection="(all)", _self=cmd):
    cmd = _self
    s = tmp_sele
    cmd.select(s, selection)
    polar_contacts = _get_polar_contacts_name(s, _self)
    _prepare(s, polar_contacts, _self=cmd)
    cmd.dss(s, preserve=1)
    cmd.cartoon("auto", s)
    cmd.show("cartoon", s)
    cmd.show("sticks", "(" + lig_sele + " and (" + s + "))")
    cmd.show("nb_spheres",
             "((" + lig_sele + "|resn hoh+wat+h2o) and (" + s + "))")
    util.cbc("(" + lig_sele + " and (" + s + "))", _self=cmd)
    util.cbac("(" + lig_sele + " and (" + s + ") and not elem c)", _self=cmd)
    cmd.spectrum("count",
                 selection="(elem c and (" + s + ") and not " + lig_sele + ")")
    cmd.set("cartoon_highlight_color", -1, selection)
    cmd.set("cartoon_fancy_helices", 0, selection)
    cmd.set("cartoon_smooth_loops", 0, selection)
    cmd.set("cartoon_flat_sheets", 1, selection)
    cmd.set("cartoon_side_chain_helper", 0, selection)
    if polar_contacts in cmd.get_names():
        cmd.disable(polar_contacts)
    if cmd.count_atoms(s):
        cmd.zoom(s)
Пример #3
0
def ligands(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 + ")")

        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("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("nonbonded", 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()
Пример #4
0
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)
Пример #5
0
def simple(selection="(all)",_self=cmd):
    cmd=_self
    s = tmp_sele
    cmd.select(s,selection)
    _prepare(s,_self=cmd)
    util.cbc(s,_self=cmd)
    cmd.show("ribbon",s)
    cmd.show("lines","(byres (("+s+" & r. CYS+CYX & n. SG) & bound_to ("+s+" & r. CYS+CYX & n. SG))) & n. CA+CB+SG")
    # try to show what covalent ligands are connected to...
    cmd.show("sticks","("+lig_sele+" and ("+s+")) extend 2")
    cmd.show("sticks","byres (("+lig_sele+" and ("+s+") and not resn ACE+NAC+NME+NH2) extend 1)")
    cmd.hide("sticks","("+s+") and ((not rep sticks) extend 1)")
    cmd.show("sticks","("+lig_sele+" and ("+s+")) extend 2")
    # color by atom if lines or sticks are shown
    util.cnc("(( rep lines or rep sticks or ("+lig_and_solv_sele+")) and ("+s+"))",_self=cmd)
    cmd.show("nonbonded","("+lig_and_solv_sele+" and ("+s+"))")
    cmd.show("lines","("+lig_and_solv_sele+" and ("+s+"))")
    if cmd.count_atoms(s):
        cmd.zoom(s)
    cmd.delete(s)
Пример #6
0
def technical(selection="(all)",_self=cmd):
    cmd=_self
    s = tmp_sele
    cmd.select(s,selection)
    polar_contacts = _get_polar_contacts_name(s,_self)
    _prepare(s,polar_contacts,_self=cmd)
    util.chainbow(s,_self=cmd)
    util.cbc("("+lig_sele+" and ("+s+"))",_self=cmd)   
    util.cbac("(("+s+") and not elem c)",_self=cmd)
    cmd.show("nonbonded",s)
    cmd.show("lines","((("+s+") and not "+lig_sele+") extend 1)")
    cmd.show("sticks","("+lig_sele+" and ("+s+"))")
    cmd.show("ribbon",s)
    cmd.dist(polar_contacts,s,s,mode=2,label=0,reset=1) # hbonds
    if polar_contacts in cmd.get_names():
        cmd.enable(polar_contacts)
        cmd.set("dash_width",1.5,polar_contacts)
        cmd.hide("labels",polar_contacts)
        cmd.show("dashes",polar_contacts)
    cmd.show("nonbonded","(("+lig_sele+"|resn hoh+wat+h2o) and ("+s+"))")
Пример #7
0
def technical(selection="(all)", _self=cmd):
    cmd = _self
    s = tmp_sele
    cmd.select(s, selection)
    polar_contacts = _get_polar_contacts_name(s, _self)
    _prepare(s, polar_contacts, _self=cmd)
    util.chainbow(s, _self=cmd)
    util.cbc("(" + lig_sele + " and (" + s + "))", _self=cmd)
    util.cbac("((" + s + ") and not elem c)", _self=cmd)
    cmd.show("nonbonded", s)
    cmd.show("lines", "(((" + s + ") and not " + lig_sele + ") extend 1)")
    cmd.show("sticks", "(" + lig_sele + " and (" + s + "))")
    cmd.show("ribbon", s)
    cmd.dist(polar_contacts, s, s, mode=2, label=0, reset=1)  # hbonds
    if polar_contacts in cmd.get_names():
        cmd.enable(polar_contacts)
        cmd.set("dash_width", 1.5, polar_contacts)
        cmd.hide("labels", polar_contacts)
        cmd.show("dashes", polar_contacts)
    cmd.show("nonbonded",
             "((" + lig_sele + "|resn hoh+wat+h2o) and (" + s + "))")
Пример #8
0
def pretty_solv(selection="(all)",_self=cmd):
    cmd=_self
    s = tmp_sele
    cmd.select(s,selection)
    polar_contacts = _get_polar_contacts_name(s,_self)
    _prepare(s,polar_contacts,_self=cmd)
    cmd.dss(s,preserve=1)
    cmd.cartoon("auto",s)
    cmd.show("cartoon",s)
    cmd.show("sticks","("+lig_sele+" and ("+s+"))")
    cmd.show("nb_spheres","(("+lig_sele+"|resn hoh+wat+h2o) and ("+s+"))")
    util.cbc("("+lig_sele+" and ("+s+"))",_self=cmd)
    util.cbac("("+lig_sele+" and ("+s+") and not elem c)",_self=cmd)
    cmd.spectrum("count",selection="(elem c and ("+s+") and not "+lig_sele+")")
    cmd.set("cartoon_highlight_color",-1,selection)
    cmd.set("cartoon_fancy_helices",0,selection)
    cmd.set("cartoon_smooth_loops",0,selection)
    cmd.set("cartoon_flat_sheets",1,selection)
    cmd.set("cartoon_side_chain_helper",0,selection)   
    if polar_contacts in cmd.get_names():
        cmd.disable(polar_contacts)
    if cmd.count_atoms(s):
        cmd.zoom(s)