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 surface_view(surface=None):
'''
Show the surface of the molecule in different representations
'''
glb.update()
util.cbc()
cmd.hide('all')
if surface == 'dot':
cmd.set('dot_density', 1)
cmd.show('lines', 'all')
cmd.show('dots', 'all')
elif surface == 'mesh':
cmd.set('mesh_quality', 3)
cmd.show('stick', 'all')
cmd.show('mesh', 'all')
elif surface == 'sphere':
cmd.set('sphere_scale', 0.5, 'all')
cmd.show('spheres', 'all')
cmd.show('surface', 'all')
cmd.set('transparency', 0.5, 'all')
elif surface == 'stick':
cmd.show('stick', 'all')
cmd.show('surface', 'all')
cmd.set('transparency', 0.5, 'all')
elif surface == 'toon':
cmd.set('cartoon_smooth_loops', 0)
cmd.show('cartoon', 'all')
cmd.show('surface', 'all')
cmd.set('transparency', 0.5, 'all')
else:
cmd.show('surface', 'all')
def surface_view(surface = None):
'''
Show the surface of the molecule in different representations
'''
glb.update()
util.cbc()
cmd.hide('all')
if surface == 'dot':
cmd.set('dot_density',1)
cmd.show('lines','all')
cmd.show('dots','all')
elif surface == 'mesh':
cmd.set('mesh_quality',3)
cmd.show('stick','all')
cmd.show('mesh','all')
elif surface == 'sphere':
cmd.set('sphere_scale',0.5,'all')
cmd.show('spheres','all')
cmd.show('surface','all')
cmd.set('transparency',0.5,'all')
elif surface == 'stick':
cmd.show('stick','all')
cmd.show('surface','all')
cmd.set('transparency',0.5,'all')
elif surface == 'toon':
cmd.set('cartoon_smooth_loops', 0)
cmd.show('cartoon','all')
cmd.show('surface','all')
cmd.set('transparency',0.5,'all')
else:
cmd.show('surface','all')
def prepare_pymol():
cmd.clip("near", 100000)
cmd.clip("slab", 100000)
cmd.clip("far", -100000)
cmd.show("spheres")
cmd.unpick()
util.cbc()
def pre_cartoon_view(tag):
if tag == 'Cartoon':
cartoon_view()
elif tag == 'Putty':
cartoon_view('putty')
elif tag == 'Lines on Cartoon':
stick_toon()
elif tag == 'Color by Chain':
util.cbc()
def pre_cartoon_view(tag):
if tag == 'Cartoon':
cartoon_view()
elif tag == 'Putty':
cartoon_view('putty')
elif tag == 'Lines on Cartoon':
stick_toon()
elif tag == 'Color by Chain':
util.cbc()
def find_and_show_interface() :
cmd.show( 'cartoon' )
cmd.hide( 'lines', 'elem H' )
cmd.set('cartoon_transparency','0.5')
util.cbc("elem C")
loaded_objs = cmd.get_names('objects')
create_interface_selections()
for obj in loaded_objs :
cmd.show( "sticks", obj+"intres" )
cmd.hide( 'sticks', 'elem H' )
def contrastinterface( pdb4char ) :
cmd.show( 'cartoon' )
cmd.hide( 'lines' )
util.cbc( 'elem C' )
cmd.set('cartoon_transparency','0.5')
v3_lines = open( "/home/andrew/rosetta/interface_seqrec_benchmark/pdbs/v3/interface_definitions/" + pdb4char + "_dsintdef.txt" ).readlines()
# benlines = open( "/home/andrew/rosetta/interface_seqrec_benchmark/pdbs/ben8Acut/interface_definitions/" + pdb4char + "_dsintdef.txt" ).readlines()
# benlines = open( "/home/andrew/rosetta/interface_seqrec_benchmark/pdbs/benV3dup_A/interface_definitions/" + pdb4char + "_dsintdef.txt" ).readlines()
# benlines = open( "/home/andrew/rosetta/interface_seqrec_benchmark/pdbs/benV3dup_B/interface_definitions/" + pdb4char + "_dsintdef.txt" ).readlines()
benlines = open( "/home/andrew/rosetta/interface_seqrec_benchmark/pdbs/benV3dup_C/interface_definitions/" + pdb4char + "_dsintdef.txt" ).readlines()
v3 = set({})
ben = set({})
for line in v3_lines :
v3.add( line.strip() )
for line in benlines:
ben.add( line.strip() )
v3_not_ben = v3 - ben
ben_not_v3 = ben - v3
print "v3 size:", len( v3)
print "ben size: ", len( ben)
print "v3 not ben: ", len( v3_not_ben )
print "ben not v3: ", len( ben_not_v3 )
v3mben_sel = sel_from_reschain_set( v3_not_ben )
benmv3_sel = sel_from_reschain_set( ben_not_v3 )
common_sel = sel_from_reschain_set( v3.intersection( ben ) )
print "v3mben_sel: ", v3mben_sel
print "benmv3_sel: ", benmv3_sel
if len(v3_not_ben):
cmd.select( "v3", v3mben_sel )
cmd.create( "v3obj", "v3" )
cmd.show( "sticks", "v3obj" )
cmd.color( "red", "v3obj" )
if len(ben_not_v3):
cmd.select( "ben", benmv3_sel )
cmd.create( "benobj", "ben" )
cmd.show( "sticks", "benobj" )
cmd.color( "pink", "benobj" )
if len(common_sel):
cmd.select( "common", common_sel )
cmd.create( "commonobj", "common" )
cmd.show( "sticks", "commonobj" )
cmd.hide( "sticks", "elem H" )
def prepare_pymol():
cmd.set("ray_trace_color", "black")
cmd.set("ray_trace_gain", 0)
cmd.set("ray_trace_mode", 3)
cmd.set("depth_cue", 0)
cmd.clip("near", 100000)
cmd.clip("slab", 100000)
cmd.clip("far", -100000)
cmd.hide("all")
util.cbc()
cmd.show('surface')
cmd.bg_color("black")
cmd.zoom("all", buffer=2.0) # buffer might help clipping problem
cmd.center("all")
cmd.deselect()
def zn_interface():
cmd.show( 'cartoon' )
cmd.hide( 'lines', 'elem H' )
util.cbc("elem C")
cmd.show( 'sticks', 'resn znx')
cmd.set('cartoon_transparency','0.5')
cmd.hide( 'sticks', 'elem H' )
loaded_objs = cmd.get_names('objects')
print loaded_objs
for obj in loaded_objs :
cmd.dist( '"'+obj+'_polar_conts"','"'+obj+'"','"'+obj+'"',quiet=1,mode=2,label=0,reset=1)
cmd.enable("'"+obj+'_polar_conts"')
def showinterface( intdef_file ):
cmd.show( 'cartoon' )
#get rid of old stuffs
cmd.hide( 'lines' )
cmd.hide( 'sticks' )
lines = open( intdef_file ).readlines()
for line in lines :
selset = 'res ' + line.split(" " )[1][:-1] + ' and chain ' + line.split(" " )[ 0 ]
#print selset
cmd.show( 'sticks', selset )
cmd.set('cartoon_transparency','0.4')
util.cbc("elem C") #colors by chain
cmd.hide( 'sticks', 'elem H' )
cmd.hide( 'lines', 'elem H' )
def reinitPymol(self, pdb):
if len(self.pdb) == 4 and self.pdb == re.match('[a-zA-Z0-9]*',
self.pdb).group(0):
cmd.delete(self.pdb)
if len(pdb) == 4 and pdb == re.match('[a-zA-Z0-9]*', pdb).group(0):
self.pdb = pdb
cmd.fetch(self.pdb, async=0)
if self.editMolecule:
cmd.hide('everything', 'all')
cmd.show('cartoon', 'all')
# color each chain differently
if self.editMolecule:
util.cbc()
# set origin at camera
if self.naturalRotation:
self.setOriginAtCamera()
# move slab away to give a comfortable viewing area
cmd.clip('move', 10)
def initPymol(self):
# set stereo mode
cmd.set('stereo_mode', 3)
cmd.stereo()
# get rid of gui
cmd.set('internal_gui', 0)
# set resolution to HD for rift
cmd.viewport(1920, 1080)
# full screen?
if self.fullscreen:
cmd.full_screen('on')
# load pdb
if len(self.pdb) == 4 and self.pdb == re.match('[a-zA-Z0-9]*',
self.pdb).group(0):
cmd.fetch(self.pdb, async=0)
if self.editMolecule == True:
cmd.hide('everything', 'all')
cmd.show('cartoon', 'all')
# color each chain differently
if self.editMolecule:
util.cbc()
# set origin at camera
if self.naturalRotation:
self.setOriginAtCamera()
# move slab away to give a comfortable viewing area
cmd.clip('move', 10)
# jiggle the camera to deal with blank screen error
cmd.move('z', .0001)
]
def do_select(self,name):
pymol.stored.link = ''
cmd.iterate(name,"stored.link=custom")
if len(pymol.stored.link):
webbrowser.open(pymol.stored.link)
cmd.delete(name)
# load an example structure
cmd.load("$TUT/1hpv.pdb")
# color by chain (aesthetics)
util.cbc()
# store the links as atom text_types
cmd.alter("name ca",r"custom='http://delsci.info/cgi-bin/click.cgi?residue=%s%s%s'%(resn,resi,chain)")
# put the mouse into single-atom selection mode
cmd.set('mouse_selection_mode',0)
# just show ribbon (means we can only select labelled C-alphas)
cmd.show_as("cartoon")
# set up the labels
def do_select(self, name):
pymol.stored.link = ''
cmd.iterate(name, "stored.link=custom")
if len(pymol.stored.link):
webbrowser.open(pymol.stored.link)
cmd.delete(name)
# load an example structure
cmd.load("$TUT/1hpv.pdb")
# color by chain (aesthetics)
util.cbc()
# store the links as atom text_types
cmd.alter(
"name CA",
r"custom='http://delsci.info/cgi-bin/click.cgi?residue=%s%s%s'%(resn,resi,chain)"
)
# put the mouse into single-atom selection mode
cmd.set('mouse_selection_mode', 0)
# just show ribbon (means we can only select labelled C-alphas)
cmd.show_as("cartoon")