def publication(selection="(all)",_self=cmd):
cmd=_self
pub_solv(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.hide("nb_spheres","(("+lig_sele+"|resn hoh+wat+h2o) and "+s+")")
cmd.delete(s)
def simple_no_solv(selection="(all)",_self=cmd):
cmd=_self
simple(selection,_self=_self)
s = tmp_sele
cmd.select(s,selection)
cmd.hide("nonbonded","("+solv_sele+" and "+s+")")
cmd.delete(s)
def pretty(selection,_self=cmd):
cmd=_self
pretty_solv(selection,_self)
s = tmp_sele
cmd.select(s,selection)
cmd.hide("nb_spheres","("+s+" and "+lig_sele+"|resn hoh+wat+h2o)")
cmd.delete(s)
def _prepare(selection,polar_contacts=None,_self=cmd):
cmd=_self
# this function should undo everything that is done by any preset function in this module
# (except for coloring)
s = tmp_sele
cmd.select(s,selection)
cmd.cartoon("auto",s)
cmd.hide("everything",s)
cmd.set("two_sided_lighting",0) # global
cmd.unset("transparency",s)
cmd.unset("dot_normals",s)
cmd.unset("mesh_normals",s)
cmd.unset("surface_quality",s)
cmd.unset("surface_type",selection)
cmd.unset("sphere_scale",selection)
cmd.unset_bond("stick_radius",s,s)
cmd.unset_bond("stick_color",s,s)
cmd.unset("cartoon_highlight_color",selection)
cmd.unset("cartoon_fancy_helices",selection)
cmd.unset("cartoon_smooth_loops",selection)
cmd.unset("cartoon_flat_sheets",selection)
cmd.unset("cartoon_side_chain_helper",selection)
cmd.unset("mesh_normals",s)
cmd.unset("dot_normals",s)
if polar_contacts == None:
polar_contacts = _get_polar_contacts_name(s,_self)
if polar_contacts in cmd.get_names('objects'):
cmd.delete(polar_contacts)
def publication(selection="(all)", _self=cmd):
cmd = _self
pub_solv(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.hide("nb_spheres",
"((" + lig_sele + "|resn hoh+wat+h2o) and " + s + ")")
def _prepare(selection, polar_contacts=None, _self=cmd):
cmd = _self
# this function should undo everything that is done by any preset function in this module
# (except for coloring)
s = tmp_sele
cmd.select(s, selection)
cmd.cartoon("auto", s)
cmd.hide("everything", s)
cmd.set("two_sided_lighting", 0) # global
cmd.unset("transparency", s)
cmd.unset("dot_normals", s)
cmd.unset("mesh_normals", s)
cmd.unset("surface_quality", s)
cmd.unset("surface_type", selection)
cmd.unset("sphere_scale", selection)
cmd.unset_bond("stick_radius", s, s)
cmd.unset_bond("stick_color", s, s)
cmd.unset("cartoon_highlight_color", selection)
cmd.unset("cartoon_fancy_helices", selection)
cmd.unset("cartoon_smooth_loops", selection)
cmd.unset("cartoon_flat_sheets", selection)
cmd.unset("cartoon_side_chain_helper", selection)
cmd.unset("mesh_normals", s)
cmd.unset("dot_normals", s)
if polar_contacts == None:
polar_contacts = _get_polar_contacts_name(s, _self)
if polar_contacts in cmd.get_names('objects'):
cmd.delete(polar_contacts)
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_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 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 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 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_cgos(mode=-1):
global cgos
if mode < 0:
cgos = not cgos
else:
cgos = mode
if cgos:
cmd.show("cgo")
else:
cmd.hide("cgo")
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 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 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_labels(mode=-1):
global labels
if mode < 0:
labels = not labels
else:
labels = mode
if labels:
cmd.show("labels")
else:
cmd.hide("labels")
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 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_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 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()
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_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 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 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+"))")
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 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 colorByRMSD(objSel1, objSel2, doAlign="True", doPretty=None):
"""
colorByRMSD -- align two structures and show the structural deviations
in color to more easily see variable regions.
PARAMS
objSel1 (valid PyMOL object or selection)
The first object to align.
objSel2 (valid PyMOL object or selection)
The second object to align
doAlign (boolean, either True or False)
Should this script align your proteins or just leave them as is?
If doAlign=True then your original proteins are aligned.
If False, then they are not. Regardless, the B-factors are changed.
DEFAULT: True
doPretty (boolean, either True or False)
If doPretty=True then a simple representation is created to
highlight the differences. If False, then no changes are made.
DEFAULT: False
RETURNS
None.
SIDE-EFFECTS
Modifies the B-factor columns in your original structures.
"""
# First create backup copies; names starting with __ (underscores) are
# normally hidden by PyMOL
tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
if strTrue(doAlign):
# perform the alignment
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
cmd.super( tObj1, tObj2, object=aln )
cmd.matrix_copy(tObj1, objSel1)
else:
# perform the alignment
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
cmd.super( tObj1, tObj2, 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=-10")
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 = [], []
# Get the residue identifiers from the alignment object "aln"
cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAres.append(resi)")
cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBres.append(resi)")
# Change the B-factors for EACH object
rmsUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
# Store the NEW B-factors
stored.alnAnb, stored.alnBnb = [], []
cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAnb.append(b)" )
cmd.iterate(tObj2 + " and n. CA and " + aln, "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 "\nColorByRMSD completed successfully."
print "The MINIMUM RMSD value is: "+str(min(stored.allRMSDval))
print "The MAXIMUM RMSD value is: "+str(max(stored.allRMSDval))
if doPretty!=None:
# Showcase what we did
cmd.orient()
cmd.hide("all")
cmd.show_as("cartoon", objSel1 + " or " + objSel2)
# Select the residues not used for alignment; they still have their B-factors as "-10"
cmd.select("notUsedForAln", "b < 0")
# White-wash the residues not used for alignment
cmd.color("white", "notUsedForAln")
# Color the residues used for alignment according to their B-factors (RMSD values)
cmd.spectrum("b", 'rainbow', "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
# 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 below.
cmd.delete("notUsedForAln")
# cmd.disable("notUsedForAln")
print "\nObjects are now colored by C-alpha RMS deviation."
print "All residues with RMSD values greater than the maximum are colored white..."
def colorByRMSD(objSel1, objSel2, doAlign="True", doPretty=None):
"""
colorByRMSD -- align two structures and show the structural deviations
in color to more easily see variable regions.
PARAMS
objSel1 (valid PyMOL object or selection)
The first object to align.
objSel2 (valid PyMOL object or selection)
The second object to align
doAlign (boolean, either True or False)
Should this script align your proteins or just leave them as is?
If doAlign=True then your original proteins are aligned.
If False, then they are not. Regardless, the B-factors are changed.
DEFAULT: True
doPretty (boolean, either True or False)
If doPretty=True then a simple representation is created to
highlight the differences. If False, then no changes are made.
DEFAULT: False
RETURNS
None.
SIDE-EFFECTS
Modifies the B-factor columns in your original structures.
"""
# First create backup copies; names starting with __ (underscores) are
# normally hidden by PyMOL
tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"
if strTrue(doAlign):
# perform the alignment
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
cmd.super( tObj1, tObj2, object=aln )
cmd.matrix_copy(tObj1, objSel1)
else:
# perform the alignment
cmd.create( tObj1, objSel1 )
cmd.create( tObj2, objSel2 )
cmd.super( tObj1, tObj2, 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=-10")
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 = [], []
# Get the residue identifiers from the alignment object "aln"
cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAres.append(resi)")
cmd.iterate(tObj2 + " and n. CA and " + aln, "stored.alnBres.append(resi)")
# Change the B-factors for EACH object
rmsUpdateB(tObj1,stored.alnAres,tObj2,stored.alnBres)
# Store the NEW B-factors
stored.alnAnb, stored.alnBnb = [], []
cmd.iterate(tObj1 + " and n. CA and " + aln, "stored.alnAnb.append(b)" )
cmd.iterate(tObj2 + " and n. CA and " + aln, "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 "\nColorByRMSD completed successfully."
print "The MINIMUM RMSD value is: "+str(min(stored.allRMSDval))
print "The MAXIMUM RMSD value is: "+str(max(stored.allRMSDval))
if doPretty!=None:
# Showcase what we did
cmd.orient()
cmd.hide("all")
cmd.show_as("cartoon", objSel1 + " or " + objSel2)
# Select the residues not used for alignment; they still have their B-factors as "-10"
cmd.select("notUsedForAln", "b < 0")
# White-wash the residues not used for alignment
cmd.color("white", "notUsedForAln")
# Color the residues used for alignment according to their B-factors (RMSD values)
cmd.spectrum("b", 'rainbow', "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln")
# 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 below.
cmd.delete("notUsedForAln")
# cmd.disable("notUsedForAln")
print "\nObjects are now colored by C-alpha RMS deviation."
print "All residues with RMSD values greater than the maximum are colored white..."
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)
import cmd, sys
# 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 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_no_solv(selection="(all)", _self=cmd):
cmd = _self
simple(selection, _self=_self)
s = tmp_sele
cmd.select(s, selection)
cmd.hide("nonbonded", "(" + solv_sele + " and " + s + ")")
def pretty(selection, _self=cmd):
cmd = _self
pretty_solv(selection, _self)
s = tmp_sele
cmd.select(s, selection)
cmd.hide("nb_spheres", "(" + s + " and " + lig_sele + "|resn hoh+wat+h2o)")
