def ligand_cartoon(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.set("cartoon_side_chain_helper",1,selection)
cmd.show("cartoon","rep ribbon")
cmd.hide("ribbon")
cmd.hide("surface")
def ligand_cartoon(selection="(all)", _self=cmd):
cmd = _self
ligand_sites(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.set("cartoon_side_chain_helper", 1, selection)
cmd.show("cartoon", "rep ribbon")
cmd.hide("ribbon")
cmd.hide("surface")
def ligand_sites_trans_hq(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("transparency","0.33",s)
cmd.set("surface_type",0,selection)
cmd.set("surface_quality",1,selection)
def toggle_dashes(mode=-1):
global dashes
if mode<0:
dashes = not dashes
else:
dashes = mode
if dashes:
cmd.show("dashes")
else:
cmd.hide("dashes")
def toggle_waters(mode=-1):
global waters
if mode<0:
waters = not waters
else:
waters = mode
if waters:
cmd.show("nonbonded",m4x_waters)
else:
cmd.hide("nonbonded",m4x_waters)
def toggle_sites(mode=-1):
global sites
if mode<0:
sites = not sites
else:
sites = mode
if sites:
cmd.show("lines",m4x_sites)
else:
cmd.hide("lines",m4x_sites)
def ligand_sites_trans_hq(selection="(all)", _self=cmd):
cmd = _self
ligand_sites(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.show("sticks", s + " and rep lines")
cmd.hide("lines", s + " and rep lines")
cmd.set("transparency", "0.33", s)
cmd.set("surface_type", 0, selection)
cmd.set("surface_quality", 1, selection)
def ligand_sites_dots(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("surface_type","1",selection)
cmd.set("surface_quality","1",selection)
cmd.set("dot_normals",0,s)
def toggle_labels(mode=-1):
global labels
if mode<0:
labels = not labels
else:
labels = mode
if labels:
cmd.show("labels")
else:
cmd.hide("labels")
def toggle_waters(mode=-1):
global waters
if mode < 0:
waters = not waters
else:
waters = mode
if waters:
cmd.show("nonbonded", m4x_waters)
else:
cmd.hide("nonbonded", m4x_waters)
def toggle_dashes(mode=-1):
global dashes
if mode < 0:
dashes = not dashes
else:
dashes = mode
if dashes:
cmd.show("dashes")
else:
cmd.hide("dashes")
def toggle_sites(mode=-1):
global sites
if mode < 0:
sites = not sites
else:
sites = mode
if sites:
cmd.show("lines", m4x_sites)
else:
cmd.hide("lines", m4x_sites)
def toggle_ligands(mode=-1):
global ligands
if mode < 0:
ligands = not ligands
else:
ligands = mode
if ligands:
cmd.show("sticks", m4x_ligands)
else:
cmd.hide("sticks", m4x_ligands)
def toggle_cgos(mode=-1):
global cgos
if mode < 0:
cgos = not cgos
else:
cgos = mode
if cgos:
cmd.show("cgo")
else:
cmd.hide("cgo")
def b_factor_putty(selection="(name ca or name p)",_self=cmd):
cmd=_self
s = tmp_sele
cmd.select(s,selection)
_prepare(s,_self=cmd)
cmd.select(s,"(name ca or name p) and ("+selection+")")
cmd.show("cartoon",s)
cmd.set("cartoon_flat_sheets",0,selection)
cmd.cartoon("putty",s)
cmd.spectrum("b",selection=s)
def toggle_cgos(mode=-1):
global cgos
if mode<0:
cgos = not cgos
else:
cgos = mode
if cgos:
cmd.show("cgo")
else:
cmd.hide("cgo")
def ligand_sites_dots(selection="(all)", _self=cmd):
cmd = _self
ligand_sites(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.show("sticks", s + " and rep lines")
cmd.hide("lines", s + " and rep lines")
cmd.set("surface_type", "1", selection)
cmd.set("surface_quality", "1", selection)
cmd.set("dot_normals", 0, s)
def toggle_ligands(mode=-1):
global ligands
if mode<0:
ligands = not ligands
else:
ligands = mode
if ligands:
cmd.show("sticks",m4x_ligands)
else:
cmd.hide("sticks",m4x_ligands)
def toggle_labels(mode=-1):
global labels
if mode < 0:
labels = not labels
else:
labels = mode
if labels:
cmd.show("labels")
else:
cmd.hide("labels")
def b_factor_putty(selection="(name ca or name p)", _self=cmd):
cmd = _self
s = tmp_sele
cmd.select(s, selection)
_prepare(s, _self=cmd)
cmd.select(s, "(name ca or name p) and (" + selection + ")")
cmd.show("cartoon", s)
cmd.set("cartoon_flat_sheets", 0, selection)
cmd.cartoon("putty", s)
cmd.spectrum("b", selection=s)
def ligand_sites_mesh(selection="(all)",_self=cmd):
cmd=_self
ligand_sites(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("surface_type","2",selection)
cmd.set("surface_quality","0",selection)
cmd.set("mesh_normals",0,s)
cmd.delete(s)
def default(selection="(all)", _self=cmd):
cmd = _self
s = tmp_sele
cmd.select(s, selection)
_prepare(s, _self=cmd)
cmd.show("lines", s)
cmd.show("nonbonded", s)
color = cmd.get_object_color_index(selection)
if color < 0:
util.cbag(selection, _self=cmd)
else:
util.cnc(selection, _self=cmd)
cmd.color(str(color), "(" + s + ") and elem c")
def default(selection="(all)",_self=cmd):
cmd=_self
s = tmp_sele
cmd.select(s,selection)
_prepare(s,_self=cmd)
cmd.show("lines",s)
cmd.show("nonbonded",s)
color=cmd.get_object_color_index(selection)
if color<0:
util.cbag(selection,_self=cmd)
else:
util.cnc(selection,_self=cmd)
cmd.color(str(color),"("+s+") and elem c")
def protein_vacuum_esp(selection, mode=2, border=10.0, quiet = 1, _self=cmd):
pymol=_self._pymol
cmd=_self
if ((string.split(selection)!=[selection]) or
selection not in cmd.get_names('objects')):
print " Error: must provide an object name"
raise cmd.QuietException
obj_name = selection + "_e_chg"
map_name = selection + "_e_map"
pot_name = selection + "_e_pot"
cmd.disable(selection)
cmd.delete(obj_name)
cmd.delete(map_name)
cmd.delete(pot_name)
cmd.create(obj_name,"((polymer and ("+selection+
") and (not resn A+C+T+G+U)) or ((bymol (polymer and ("+
selection+"))) and resn NME+NHE+ACE)) and (not hydro)")
# try to just get protein...
protein_assign_charges_and_radii(obj_name,_self=_self)
ext = cmd.get_extent(obj_name)
max_length = max(abs(ext[0][0] - ext[1][0]),abs(ext[0][1] - ext[1][1]),abs(ext[0][2]-ext[1][2])) + 2*border
# compute an grid with a maximum dimension of 50, with 10 A borders around molecule, and a 1.0 A minimum grid
sep = max_length/50.0
if sep<1.0: sep = 1.0
print " Util: Calculating electrostatic potential..."
if mode==0: # absolute, no cutoff
cmd.map_new(map_name,"coulomb",sep,obj_name,border)
elif mode==1: # neutral, no cutoff
cmd.map_new(map_name,"coulomb_neutral",sep,obj_name,border)
else: # local, with cutoff
cmd.map_new(map_name,"coulomb_local",sep,obj_name,border)
cmd.ramp_new(pot_name, map_name, selection=obj_name,zero=1)
cmd.hide("everything",obj_name)
cmd.show("surface",obj_name)
cmd.set("surface_color",pot_name,obj_name)
cmd.set("surface_ramp_above_mode",1,obj_name)
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)
def ball_and_stick(selection="(all)", mode=1, _self=cmd):
cmd = _self
s = tmp_sele
cmd.select(s, selection)
_prepare(s, _self=cmd)
if mode == 1:
cmd.hide("everything", s)
cmd.set_bond("stick_color", "white", s, s)
cmd.set_bond("stick_radius", "0.14", s, s)
cmd.set("sphere_scale", "0.25", s)
cmd.show("sticks", s)
cmd.show("spheres", s)
elif mode == 2:
cmd.hide("everything", s)
cmd.set_bond("stick_color", "white", s, s)
cmd.set_bond("stick_radius", "-0.14", s, s)
cmd.set("stick_ball", "1")
cmd.set("stick_ball_ratio", -1.0)
cmd.set("stick_ball_color", "atomic")
cmd.show("sticks", s)
def ball_and_stick(selection="(all)",mode=1,_self=cmd):
cmd=_self
s = tmp_sele
cmd.select(s,selection)
_prepare(s,_self=cmd)
if mode == 1:
cmd.hide("everything",s)
cmd.set_bond("stick_color","white",s,s)
cmd.set_bond("stick_radius","0.14",s,s)
cmd.set("sphere_scale","0.25",s)
cmd.show("sticks",s)
cmd.show("spheres",s)
elif mode == 2:
cmd.hide("everything",s)
cmd.set_bond("stick_color","white",s,s)
cmd.set_bond("stick_radius","-0.14",s,s)
cmd.set("stick_ball","1")
cmd.set("stick_ball_ratio",-1.0)
cmd.set("stick_ball_color","atomic")
cmd.show("sticks",s)
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)
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+"))")
def setup_contexts(context_info): # Author: Warren DeLano
(list, dict) = context_info[0:2]
key_list = [
'F1',
'F2',
'F3',
'F4',
'F5',
'F6',
'F7',
'F8',
'F9',
'F10', #,'F11','F12',
'SHFT-F1',
'SHFT-F2',
'SHFT-F3',
'SHFT-F4',
'SHFT-F5',
'SHFT-F6',
'SHFT-F7',
'SHFT-F8',
'SHFT-F9',
'SHFT-F10'
] # ,'SHFT-F11','SHFT-F12']
doc_list = ["Keys"]
zoom_context = 1
global labels
labels = 1
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, toggle_labels)
doc_list.append(key + ": Toggle Dist")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key, lambda: (cmd.zoom(), toggle_labels(0)))
doc_list.append(key + ": Zoom All")
for a in list:
water = a + "_water"
ligand = a + "_ligand"
site = a + "_site"
hbond = a + "_hbond"
name_list = dict[a]
zoom_list = []
if water in name_list:
cmd.show("nonbonded", water)
util.cbac(water)
zoom_list.append(water)
if ligand in name_list:
cmd.show("sticks", ligand)
cmd.hide("cartoon", ligand)
util.cbag(ligand)
zoom_list.append(ligand)
if site in name_list:
cmd.show("sticks", site)
util.cbac(site)
zoom_list.append(site)
# replace cartoon with explicit atoms for "site" atoms
cmd.hide("cartoon", site)
cmd.show(
"sticks",
"(byres (neighbor (" + site + " and name c))) and name n+ca")
cmd.show(
"sticks",
"(byres (neighbor (" + site + " and name n))) and name c+ca+o")
if len(zoom_list):
if len(key_list):
key = key_list.pop(0)
zoom_str = string.join(zoom_list, ' or ')
if zoom_context == 1:
zoom_context = zoom_str
elif zoom_context not in (0, 1):
zoom_context = 0
cmd.set_key(key, lambda x=zoom_str: (cmd.zoom(x)))
mo = re.search("_([^_]+)$", a)
if mo:
cont_name = mo.groups()[0]
else:
cont_name = a
doc_list.append(key + ": Zoom " + cont_name)
if hbond in name_list:
cmd.show("dashes", hbond)
cmd.show("labels", hbond)
cmd.wizard("fedora", doc_list)
if zoom_context not in (0, 1):
cmd.zoom(zoom_context)
toggle_labels(0)
# cmd.feedback("enable","python","output")
cmd.feedback("enable", "objectmolecule", "results")
cmd.feedback("disable", "selector", "actions")
cmd.feedback("disable", "scene", "actions")
cmd.set("internal_feedback", 1)
cmd.set("internal_prompt", 0)
def setup_contexts(context_info): # Author: Warren DeLano
(list,dict) = context_info[0:2]
key_list = [
'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10', #,'F11','F12',
'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7',
'SHFT-F8','SHFT-F9','SHFT-F10']# ,'SHFT-F11','SHFT-F12']
doc_list = ["Keys"]
zoom_context = 1
global labels
labels = 1
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_labels)
doc_list.append(key+": Toggle Dist")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,lambda :(cmd.zoom(),toggle_labels(0)))
doc_list.append(key+": Zoom All")
for a in list:
water = a+"_water"
ligand = a+"_ligand"
site = a+"_site"
hbond = a+"_hbond"
name_list = dict[a]
zoom_list = []
if water in name_list:
cmd.show("nonbonded",water)
util.cbac(water)
zoom_list.append(water)
if ligand in name_list:
cmd.show("sticks",ligand)
cmd.hide("cartoon",ligand)
util.cbag(ligand)
zoom_list.append(ligand)
if site in name_list:
cmd.show("sticks",site)
util.cbac(site)
zoom_list.append(site)
# replace cartoon with explicit atoms for "site" atoms
cmd.hide("cartoon",site)
cmd.show("sticks","(byres (neighbor ("+site+" and name c))) and name n+ca")
cmd.show("sticks","(byres (neighbor ("+site+" and name n))) and name c+ca+o")
if len(zoom_list):
if len(key_list):
key = key_list.pop(0)
zoom_str = string.join(zoom_list,' or ')
if zoom_context == 1:
zoom_context = zoom_str
elif zoom_context not in (0,1):
zoom_context = 0
cmd.set_key(key,lambda x=zoom_str:(cmd.zoom(x)))
mo = re.search("_([^_]+)$",a)
if mo:
cont_name = mo.groups()[0]
else:
cont_name = a
doc_list.append(key+": Zoom "+cont_name)
if hbond in name_list:
cmd.show("dashes",hbond)
cmd.show("labels",hbond)
cmd.wizard("fedora",doc_list)
if zoom_context not in (0,1):
cmd.zoom(zoom_context)
toggle_labels(0)
# cmd.feedback("enable","python","output")
cmd.feedback("enable","objectmolecule","results")
cmd.feedback("disable","selector","actions")
cmd.feedback("disable","scene","actions")
cmd.set("internal_feedback",1)
cmd.set("internal_prompt",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()
def ColorByDisplacementCA(objSel1, objSel2, super1='all', super2='all', doColor="True", doAlign="True", AlignedWhite='yes'):
### First create backup copies; names starting with __ (underscores) are normally hidden by PyMOL
tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
if strTrue(doAlign):
### Create temp objects
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
### Align and make create an object aln which indicates which atoms were paired between the two structures
### Super is must faster than align http://www.pymolwiki.org/index.php/Super
cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln)
### Modify the original matrix of object1 from the alignment
cmd.matrix_copy(tObj1, objSel1)
else:
### Create temp objects
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
### Align and make create an object aln which indicates which atoms were paired between the two structures
### Super is must faster than align http://www.pymolwiki.org/index.php/Super
cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln)
### Modify the B-factor columns of the original objects,
### in order to identify the residues NOT used for alignment, later on
cmd.alter( objSel1 + " or " + objSel2, "b=-0.2")
cmd.alter( tObj1 + " or " + tObj2, "chain='A'")
cmd.alter( tObj1 + " or " + tObj2, "segi='A'")
### Update pymol internal representations; one of these should do the trick
cmd.refresh(); cmd.rebuild(); cmd.sort(tObj1); cmd.sort(tObj2)
### Create lists for storage
stored.alnAres, stored.alnBres = [], []
### Iterate over objects
if AlignedWhite=='yes':
cmd.iterate(tObj1 + " and n. CA and not " + aln, "stored.alnAres.append(resi)")
cmd.iterate(tObj2 + " and n. CA and not " + aln, "stored.alnBres.append(resi)")
else:
cmd.iterate(tObj1 + " and n. CA", "stored.alnAres.append(resi)")
cmd.iterate(tObj2 + " and n. CA", "stored.alnBres.append(resi)")
### Change the B-factors for EACH object
displacementUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
### Store the NEW B-factors
stored.alnAnb, stored.alnBnb = [], []
### Iterate over objects and get b
if AlignedWhite=='yes':
### Iterate over objects which is not aligned
cmd.iterate(tObj1 + " and n. CA and not " + aln, "stored.alnAnb.append(b)" )
cmd.iterate(tObj2 + " and n. CA and not " + aln, "stored.alnBnb.append(b)" )
else:
### Or Iterate over all objects with CA
cmd.iterate(tObj1 + " and n. CA", "stored.alnAnb.append(b)" )
cmd.iterate(tObj2 + " and n. CA", "stored.alnBnb.append(b)" )
### Get rid of all intermediate objects and clean up
cmd.delete(tObj1)
cmd.delete(tObj2)
cmd.delete(aln)
### Assign the just stored NEW B-factors to the original objects
for x in range(len(stored.alnAres)):
cmd.alter(objSel1 + " and n. CA and i. " + str(stored.alnAres[x]), "b = " + str(stored.alnAnb[x]))
for x in range(len(stored.alnBres)):
cmd.alter(objSel2 + " and n. CA and i. " + str(stored.alnBres[x]), "b = " + str(stored.alnBnb[x]))
cmd.rebuild(); cmd.refresh(); cmd.sort(objSel1); cmd.sort(objSel2)
### Provide some useful information
stored.allRMSDval = []
stored.allRMSDval = stored.alnAnb + stored.alnBnb
print "\nColorByDisplacementCA completed successfully."
print "The MAXIMUM Displacement is: "+str(max(stored.allRMSDval)) +" residue "+str(stored.alnAres[int(stored.allRMSDval.index(max(stored.allRMSDval)))])
if strTrue(doColor):
### Showcase what we did
#cmd.orient()
#cmd.hide("all")
cmd.show("cartoon", objSel1 + " or " + objSel2)
### Select the residues not used for alignment; they still have their B-factors as "-0.2"
cmd.select("notUsedForAln", "b = -0.2")
### White-wash the residues not used for alignment
cmd.color("white", "notUsedForAln")
### Select the residues not in both pdb files; they have their B-factors as "-0. 01"
cmd.select("ResNotInBothPDB", "b = -0.01")
### White-wash the residues not used for alignment
cmd.color("black", "ResNotInBothPDB")
### Color the residues used for alignment according to their B-factors (Displacment values)
# cmd.spectrum("b", 'rainbow', "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln+ResNotInBothPDB")
cmd.spectrum("b", 'rainbow', "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not (notUsedForAln or ResNotInBothPDB)")
### Delete the selection of atoms not used for alignment
### If you would like to keep this selection intact,
### just comment "cmd.delete" line and
### uncomment the "cmd.disable" line abowe.
cmd.disable("notUsedForAln")
cmd.delete("notUsedForAln")
cmd.disable("ResNotInBothPDB")
cmd.delete("ResNotInBothPDB")
print "\nObjects are now colored by C-alpha displacement deviation."
print "Blue is minimum and red is maximum..."
print "White is those residues used in the alignment algorithm. Can be turned off in top of algorithm."
print "Black is residues that does not exist in both files..."
# This is a set of in-line functions used to specify color gradients. fx is
# the fractional time of a given step within the trajectories (ranging from 0
# to 1). "color_graidents" is a list of references to these functions.
# If multiple trajectories are loaded, the gradients are applied in the order
# specified in color_gradients. The trajectories are ordered by where they
# occur in the command line.
def a(fx): return [fx,0,(1.0-fx)] #fx,fx,1-fx]
def b(fx): return [1,fx,1] #1,fx,fx]
def c(fx): return [1,1,fx] #1-fx,1-fx,fx]
color_gradients = [a,b,c]
# Default representations
cmd.hide("everything","all")
cmd.show("ribbon","all")
cmd.show("spheres","resn N06 or resn N15 or resn E40 or resn EST")
# Create a list of unique trajectories loaded by parsing the command line
unique = [arg[:-4] for arg in sys.argv if arg.endswith(".pdb")]
# Go through each trajecotry
models = cmd.get_names("all")
for i, u in enumerate(unique):
traj = [m for m in models if "_".join(m.split("_")[:-1]) == u]
# Go through each step in the trajectory
num_steps = float(len(traj))
for j, t in enumerate(traj):
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)
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 + "))")
return [fx, 0, (1.0 - fx)] #fx,fx,1-fx]
def b(fx):
return [1, fx, 1] #1,fx,fx]
def c(fx):
return [1, 1, fx] #1-fx,1-fx,fx]
color_gradients = [a, b, c]
# Default representations
cmd.hide("everything", "all")
cmd.show("ribbon", "all")
cmd.show("spheres", "resn N06 or resn N15 or resn E40 or resn EST")
# Create a list of unique trajectories loaded by parsing the command line
unique = [arg[:-4] for arg in sys.argv if arg.endswith(".pdb")]
# Go through each trajecotry
models = cmd.get_names("all")
for i, u in enumerate(unique):
traj = [m for m in models if "_".join(m.split("_")[:-1]) == u]
# Go through each step in the trajectory
num_steps = float(len(traj))
for j, t in enumerate(traj):
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)
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()
