def pretty_protein(sele="(all)"):
"""DESCRIPTION
This is my default display. It displays the protein as cartoon, but
highlights ligands and ions as sticks or spheres.
USAGE
pretty_protein [selection]
AUTHOR
Spencer Bliven
"""
cmd.hide("lines",sele)
cmd.hide("everything","( %s ) and solvent"%sele)
cmd.show("cartoon",sele)
# disulfides
cmd.show("sticks","( %s ) and (cys/ca+cb+sg) and byres (cys/sg and bound_to cys/sg)"%sele)
# ligands
cmd.show("sticks","( %s ) and hetatm and not solvent and not hydrogen and not resn MSE"%sele)
# metals
cmd.show("spheres","( %s ) and not elem c+n+o+h+s and not resn MSE"%sele)
# color carbon by chain & others by element
util.cbc(sele)
util.cnc(sele)
def Show_Results(self):
i = 0
for key in sorted(self.dictSimData.keys()):
Result = self.ResultsContainer.Get_ResultID(key)
if Result is not None:
try:
ResultID = str(
Result.ResultID) if Result.ResultID != -1 else 'REF'
ResultName = 'RESULT_' + ResultID + '__'
ResultHBondsName = 'RESULT_' + ResultID + '_H_BONDS__'
cmd.load(Result.ResultFile, ResultName, state=1)
cmd.refresh()
cmd.color(self.PymolColorList[i], ResultName)
util.cnc(ResultName)
cmd.refresh()
self.Nice_Display(Result, ResultName)
self.Highlight_HBonds(Result, ResultName, ResultHBondsName)
except:
continue
i += 1
def EditView(self):
#Display the ligand with the new coordinates
#print "will load " + self.LigandObj + " in state " + str(self.State)
try:
cmd.load(self.top.listTmpPDB[self.TOP + 1], self.LigandObj,
self.State)
cmd.refresh()
# No flexible side-chain(s)
if self.selSideChains == '':
selString = self.selLigand + " or " + self.selTarget
else:
selString = self.selSideChains + " or " + self.selLigand + " or " + self.selTarget
#print selString
# Create solution object
# Object contains the whole protein-ligand complex
SolutionObj = "TOP_" + str(self.TOP + 1) + "__"
cmd.create(SolutionObj, selString, self.State, self.State)
cmd.refresh()
# Color ligand of solution TOP
Selection = "(resn LIG & " + SolutionObj + " & present)"
cmd.color(self.top.top.PymolColorList[self.TOP], Selection)
util.cnc(Selection)
cmd.refresh()
# Color side-chains of solution TOP
if self.selSideChains != '':
selSC = self.selSideChains.replace(self.TargetObj, SolutionObj)
cmd.color(self.top.top.PymolColorList[self.TOP], selSC)
util.cnc(selSC)
cmd.refresh()
#cmd.show(self.DefaultDisplay, "(resn LIG & sol_*__ & present)")
cmd.show(self.top.DefaultDisplay,
"(resn LIG & " + SolutionObj + " & present)")
cmd.refresh()
if self.selSideChains != '':
#cmd.show("sticks", self.selSideChains.replace(self.TargetName__,"sol_*__"))
cmd.show(
"sticks",
self.selSideChains.replace(self.TargetObj, SolutionObj))
cmd.refresh()
except:
self.CriticalError("Could not refresh the visual display")
return 1
return 0
def EditView(self):
#Display the ligand with the new coordinates
#print "will load " + self.LigandObj + " in state " + str(self.State)
try:
cmd.load(self.top.listTmpPDB[self.TOP+1], self.LigandObj, self.State)
cmd.refresh()
# No flexible side-chain(s)
if self.selSideChains == '':
selString = self.selLigand + " or " + self.selTarget
else:
selString = self.selSideChains + " or " + self.selLigand + " or " + self.selTarget
#print selString
# Create solution object
# Object contains the whole protein-ligand complex
SolutionObj = "TOP_" + str(self.TOP+1) + "__"
cmd.create(SolutionObj, selString, self.State, self.State)
cmd.refresh()
# Color ligand of solution TOP
Selection = "(resn LIG & " + SolutionObj + " & present)"
cmd.color(self.top.top.PymolColorList[self.TOP], Selection)
util.cnc(Selection)
cmd.refresh()
# Color side-chains of solution TOP
if self.selSideChains != '':
selSC = self.selSideChains.replace(self.TargetObj,SolutionObj)
cmd.color(self.top.top.PymolColorList[self.TOP], selSC)
util.cnc(selSC)
cmd.refresh()
#cmd.show(self.DefaultDisplay, "(resn LIG & sol_*__ & present)")
cmd.show(self.top.DefaultDisplay, "(resn LIG & " + SolutionObj + " & present)")
cmd.refresh()
if self.selSideChains != '':
#cmd.show("sticks", self.selSideChains.replace(self.TargetName__,"sol_*__"))
cmd.show("sticks", self.selSideChains.replace(self.TargetObj,SolutionObj))
cmd.refresh()
except:
self.CriticalError("Could not refresh the visual display")
return 1
return 0
def finalCosmetics(self): #make everything look nice
for ensemble in self.currentLabel.ensembles:
if len(self.currentLabel.ensembles[ensemble].rotamers) > 0:
#show all conformations and do some coloring
cmd.set("all_states", 1)
self.toggleStatesCaption = 'Toggle states: ON'
cmd.color(
"blue",
"%s_%s_%s" % (self.residue1Name,
self.currentLabel.identifier, ensemble))
cmd.color(
"red", "%s_%s_%s & name %s" %
(self.residue1Name, self.currentLabel.identifier, ensemble,
self.currentLabel.highlight))
util.cnc("%s_%s_%s" % (self.residue1Name,
self.currentLabel.identifier, ensemble))
identifierLabel = "%s|%s|%s|%s|%s" % (
self.residue1Name, self.currentLabel.identifier,
self.vdwRestraints, self.thoroughness, ensemble)
#pseudoatom at average N1 position
stored.label = []
cmd.iterate_state(
0, "%s_%s_%s & name %s" %
(self.residue1Name, self.currentLabel.identifier, ensemble,
self.currentLabel.spinLocation),
'stored.label.append((x,y,z))')
atoms1 = numpy.array(stored.label)
#create pseudoatom at average coordinate of each ensemble
avgAtoms = numpy.average(atoms1, axis=0)
self.createPseudoatom(
avgAtoms, "%s_%s_label" % (self.residue1Name, ensemble), 1)
cmd.set("sphere_scale", "0.5",
"%s_%s_label" % (self.residue1Name, ensemble))
cmd.label("%s_%s_label" % (self.residue1Name, ensemble),
` identifierLabel `)
cmd.show("label")
cmd.show("spheres", "name PS1")
cmd.group(
"%s%s" % (self.object_prefix, str(self.numberOfLabel)),
"%s*, labelEnvironment_%s,%s*" %
("currentLabel", "currentLabel", self.residue1Name))
def Nice_Display(self, Result, ResultName):
cmd.hide('everything', ResultName)
cmd.refresh()
cmd.show('cartoon', ResultName)
cmd.refresh()
for opt in Result.Optimizable:
if opt.rnc[:3] == 'LIG':
cmd.show('lines', 'byres(resn LIG around 5.0) & ' + ResultName)
res = opt.rnc[:3].replace('-', '')
num = opt.rnc[3:len(opt.rnc) - 1].replace('-', '')
chn = opt.rnc[-1:].replace('-', '')
sele = 'resn ' + res + ' & resi ' + num + ' & chain \'' + chn + '\' & ' + ResultName
cmd.show('sticks', sele)
cmd.color('white', sele)
util.cnc(ResultName)
cmd.refresh()
def color_obj(rainbow=0,cnc=1):
"""
AUTHOR
Gareth Stockwell
Modified by Spencer Bliven
USAGE
color_obj(rainbow=0, cnc=0)
ARGUMENTS
rainbow = integer: 0 to use the 22 named colors, or 1 to generate
a rainbow based on the number of objects currently
cnc = integer: 0 to color all atoms by object, 1 to color non-carbon
atoms according to their element.
NOTES
This function colours each object currently in the PyMOL heirarchy
with a different colour. Colours used are either the 22 named
colours used by PyMOL (in which case the 23rd object, if it exists,
gets the same colour as the first), or are the colours of the rainbow
If cnc is set, color non-carbon atoms by their element
SEE ALSO
util.color_objs()
"""
# Process arguments
rainbow = int(rainbow)
cnc = int(cnc)
# Get names of all PyMOL objects
obj_list = cmd.get_names('objects')
if rainbow:
print "\nColouring objects as rainbow\n"
nobj = len(obj_list)
# Create colours starting at blue(240) to red(0), using intervals
# of 240/(nobj-1)
for j in range(nobj):
hsv = (240-j*240/(nobj-1), 1, 1)
# Convert to RGB
rgb = hsv_to_rgb(hsv)
# Define the new colour
cmd.set_color("col" + str(j), rgb)
print obj_list[j], rgb
# Colour the object
cmd.color("col" + str(j), obj_list[j])
else:
print "\nColouring objects using PyMOL defined colours\n"
# List of available colours
colours = ['red', 'green', 'blue', 'yellow', 'violet', 'cyan', \
'salmon', 'lime', 'pink', 'slate', 'magenta', 'orange', 'marine', \
'olive', 'purple', 'teal', 'forest', 'firebrick', 'chocolate', \
'wheat', 'white', 'grey' ]
ncolours = len(colours)
# Loop over objects
i = 0
for obj in obj_list:
print " ", obj, colours[i]
cmd.color(colours[i], obj)
i = i+1
if(i == ncolours):
i = 0
if cnc:
#color non-carbons appropriately
util.cnc()