def testGetMoviePlaying(self):
self.prep_movie()
cmd.mplay()
self.assertEquals(cmd.get_movie_playing(),1)
cmd.mstop()
self.assertEquals(cmd.get_movie_playing(),0)
def testGetMoviePlaying(self):
self.prep_movie()
cmd.mplay()
self.assertEquals(cmd.get_movie_playing(), 1)
cmd.mstop()
self.assertEquals(cmd.get_movie_playing(), 0)
def testMtoggle(self):
self.prep_movie()
cmd.mstop()
# toggle on
cmd.mtoggle()
self.assertEquals(cmd.get_movie_playing(),1)
# toggle off
cmd.mtoggle()
self.assertEquals(cmd.get_movie_playing(),0)
def testMtoggle(self):
self.prep_movie()
cmd.mstop()
# toggle on
cmd.mtoggle()
self.assertEquals(cmd.get_movie_playing(), 1)
# toggle off
cmd.mtoggle()
self.assertEquals(cmd.get_movie_playing(), 0)
def electomo(self,cleanup=0):
if not cleanup:
cmd.feedback("disable","objectsurface","actions")
cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/flagellar.pse"))
cmd.set("sweep_mode",3)
cmd.set("sweep_angle",3)
cmd.rock()
cmd.do("replace_wizard toggle, Electron Tomography")
else:
cmd.mstop()
cmd.rock(0)
def electomo(self,cleanup=0):
if not cleanup:
cmd.feedback("disable","objectsurface","actions")
cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/flagellar.pse"))
cmd.set("sweep_mode",3)
cmd.set("sweep_angle",3)
cmd.rock()
cmd.do("replace_wizard toggle, Electron Tomography")
else:
cmd.mstop()
cmd.rock(0)
def convert_spin(self):
'''spin the protein'''
if self.argsLength > 1 and self.args[1] == 'off':
cmd.mstop()
cmd.mset()
pymSpin = 'PyMOL: mstop; mset\n\n'
else:
cmd.mset('1 x180')
util.mroll(1,180,1)
cmd.mplay()
pymSpin = 'PyMOL: mset 1 x180; util.mroll(1,180,1); mplay'
print pymSpin
def convert_spin(self):
'''spin the protein'''
if self.argsLength > 1 and self.args[1] == 'off':
cmd.mstop()
cmd.mset()
pymSpin = 'PyMOL: mstop; mset\n\n'
else:
cmd.mset('1 x180')
util.mroll(1, 180, 1)
cmd.mplay()
pymSpin = 'PyMOL: mset 1 x180; util.mroll(1,180,1); mplay'
print pymSpin
def animate(self,cleanup=0):
if not cleanup:
cmd.set("security",0)
cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/animate.pse"))
cmd.rock(1)
cmd.set("field_of_view",23)
cmd.rock(1)
cmd.set("sweep_mode",3)
cmd.set("sweep_angle",10)
cmd.do("replace_wizard toggle, Molecular Animation")
else:
cmd.set("mesh_width",1)
cmd.set("field_of_view",20)
cmd.rock(0)
cmd.mset()
cmd.mstop()
def highlight_chains():
cmd.mstop()
cmd.mclear()
cmd.mset()
glb.update()
colors = ['blue', 'orange', 'silver', 'green', 'yellow',
'purple', 'brightorange', 'lightblue', 'lightorange',
'pink', 'forest', 'firebrick', 'paleyellow', 'salmon',
'ruby', 'wheat', 'lightmagenta', 'nitblue']
chains = []
numChains = 0
objects = cmd.get_names('all')
for obj in objects:
split = obj.split('Chain-')
if len(split) == 2:
chains.append(split[1])
numChains += 1
numFrames = (numChains*200)+70
cmd.mset('1', numFrames)
cmd.mdo(1,'color red, all; hide cartoon, all')
cmd.orient()
cmd.mview('store', '1')
colorCount = 0
frameCount = 1
for i in chains:
cmd.orient('chain ' + i)
cmd.mview('store', frameCount+59)
cmd.mview('store', frameCount+115)
flash_chain(i, frameCount+59, 'red', colors[colorCount])
cmd.orient()
cmd.turn('x', '270')
cmd.turn('y', '180')
cmd.mview('store', frameCount+150)
cmd.mview('store', frameCount+170)
colorCount += 1
frameCount += 200
if(frameCount > numFrames-100):
cmd.orient()
cmd.mdo(numFrames,'mstop')
cmd.mview('store', (numChains*200)+70)
cmd.mview('interpolate')
cmd.show('ribbon')
cmd.color('red', 'all')
def animate(self,cleanup=0):
if not cleanup:
cmd.set("security",0)
cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/animate.pse"))
cmd.rock(1)
cmd.set("field_of_view",23)
cmd.rock(1)
cmd.set("sweep_mode",3)
cmd.set("sweep_angle",10)
cmd.set("sphere_mode",5)
cmd.do("replace_wizard toggle, Molecular Animation")
else:
cmd.set("mesh_width",1)
cmd.set("field_of_view",20)
cmd.rock(0)
cmd.mset()
cmd.mstop()
def ray(self,cleanup=0):
if not cleanup:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("ray")
cmd.set("sphere_scale",1.0)
cmd.load("$PYMOL_DATA/demo/il2.pdb","ray")
cmd.remove("(ray and hydro)")
cmd.hide("lines","ray")
cmd.show("spheres","ray")
cmd.orient("ray")
cmd.turn("x",90)
util.ray_shadows('heavy')
cmd.mstop()
cmd.rock(0)
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.do("ray")
else:
cmd.delete("ray")
def ray(self,cleanup=0):
if not cleanup:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("ray")
cmd.set("sphere_mode",5)
cmd.set("sphere_scale",1.0)
cmd.load("$PYMOL_DATA/demo/il2.pdb","ray")
cmd.remove("(ray and hydro)")
cmd.hide("lines","ray")
cmd.show("spheres","ray")
cmd.orient("ray")
cmd.turn("x",90)
util.ray_shadows('heavy')
cmd.mstop()
cmd.rock(0)
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.do("ray")
else:
cmd.delete("ray")
def surface_cartoon():
glb.update()
cmd.mstop()
cmd.mclear()
cmd.mset('1', '60')
cmd.hide('everything')
objects = cmd.get_names('all')
glb.procolor(None,show_all=('cartoon','surface'))
cmd.set("cartoon_fancy_helices", "1")
cmd.set("cartoon_fancy_sheets", "1")
cmd.mdo(1,'set transparency = 0.75, all;')
cmd.mdo(2,'set transparency = 0.7, all;')
cmd.mdo(3,'set transparency = 0.65, all;')
cmd.mdo(4,'set transparency = 0.6, all;')
cmd.mdo(5,'set transparency = 0.55, all;')
cmd.mdo(6,'set transparency = 0.5, all;')
cmd.mdo(7,'set transparency = 0.45, all;')
cmd.mdo(8,'set transparency = 0.4, all;')
cmd.mdo(9,'set transparency = 0.35, all;')
cmd.mdo(10,'set transparency = 0.3, all;')
cmd.mdo(11,'set transparency = 0.25, all;')
cmd.mdo(12,'set transparency = 0.2, all;')
cmd.mdo(13,'set transparency = 0.15, all;')
cmd.mdo(14,'set transparency = 0.1, all;')
cmd.mdo(15,'set transparency = 0.05, all;')
cmd.mdo(16,'set transparency = 0, all;')
cmd.mdo(17,'set transparency = 0, all;')
cmd.mdo(19,'set transparency = 0, all;')
cmd.mdo(20,'set transparency = 0, all;')
cmd.mdo(21,'set transparency = 0, all;')
cmd.mdo(22,'set transparency = 0, all;')
cmd.mdo(23,'set transparency = 0, all;')
cmd.mdo(24,'set transparency = 0, all;')
cmd.mdo(25,'set transparency = 0, all;')
cmd.mdo(26,'set transparency = 0, all;')
cmd.mdo(27,'set transparency = 0, all;')
cmd.mdo(28,'set transparency = 0, all;')
cmd.mdo(29,'set transparency = 0.05, all;')
cmd.mdo(30,'set transparency = 0.1, all;')
cmd.mdo(31,'set transparency = 0.15, all;')
cmd.mdo(32,'set transparency = 0.2, all;')
cmd.mdo(33,'set transparency = 0.25, all;')
cmd.mdo(34,'set transparency = 0.3, all;')
cmd.mdo(35,'set transparency = 0.35, all;')
cmd.mdo(36,'set transparency = 0.4, all;')
cmd.mdo(37,'set transparency = 0.45, all;')
cmd.mdo(38,'set transparency = 0.5, all;')
cmd.mdo(39,'set transparency = 0.55, all;')
cmd.mdo(40,'set transparency = 0.6, all;')
cmd.mdo(41,'set transparency = 0.65, all;')
cmd.mdo(42,'set transparency = 0.7, all;')
cmd.mdo(43,'set transparency = 0.75, all;')
cmd.mdo(44,'set transparency = 0.8, all;')
cmd.mdo(45,'set transparency = 0.85, all;')
cmd.mdo(46,'set transparency = 0.9, all;')
cmd.mdo(47,'set transparency = 0.9, all;')
cmd.mdo(48,'set transparency = 0.9, all;')
cmd.mdo(49,'set transparency = 0.85, all;')
cmd.mdo(50,'set transparency = 0.85, all;')
cmd.mdo(51,'set transparency = 0.85, all;')
cmd.mdo(52,'set transparency = 0.85, all;')
cmd.mdo(53,'set transparency = 0.85, all;')
cmd.mdo(54,'set transparency = 0.85, all;')
cmd.mdo(55,'set transparency = 0.85, all;')
cmd.mdo(56,'set transparency = 0.85, all;')
cmd.mdo(57,'set transparency = 0.85, all;')
cmd.mdo(58,'set transparency = 0.85, all;')
cmd.mdo(59,'set transparency = 0.85, all;')
cmd.mdo(60,'set transparency = 0.8, all;')
def Ligand_Pull():
glb.update()
cmd.mstop()
cmd.mclear()
cmd.mset('1', '442')
cmd.hide('everything')
cmd.remove('resn HOH')
cmd.color('green', 'all')
objects = cmd.get_names('all')
if 'ligands' in objects:
cmd.set('stick_radius', '0.3')
glb.procolor('ligands around 6','sticks','cpk','cartoon')
glb.procolor('ligands','spheres','orange',None)
cmd.set("cartoon_fancy_helices", "1")
cmd.set("cartoon_fancy_sheets", "1")
cmd.set('cartoon_transparency', '0.5')
cmd.zoom()
cmd.orient()
cmd.mdo(1,'orient')
cmd.mdo(2,'translate [2,0,0],ligands;')
cmd.mdo(3,'translate [2,0,0],ligands;')
cmd.mdo(4,'translate [2,0,0],ligands;')
cmd.mdo(5,'translate [2,0,0],ligands;')
cmd.mdo(6,'translate [2,0,0],ligands;')
cmd.mdo(7,'translate [2,0,0],ligands;')
cmd.mdo(8,'translate [2,0,0],ligands;')
cmd.mdo(9,'translate [2,0,0],ligands;')
cmd.mdo(10,'translate [2,0,0],ligands;')
cmd.mdo(11,'translate [2,0,0],ligands;')
cmd.mdo(12,'translate [2,0,0],ligands;')
cmd.mdo(13,'translate [2,0,0],ligands;')
cmd.mdo(14,'translate [2,0,0],ligands;')
cmd.mdo(15,'translate [2,0,0],ligands;')
cmd.mdo(16,'translate [2,0,0],ligands;')
cmd.mdo(17,'translate [2,0,0],ligands;')
cmd.mdo(18,'translate [2,0,0],ligands;')
cmd.mdo(19,'translate [2,0,0],ligands;')
cmd.mdo(20,'translate [2,0,0],ligands;')
cmd.mdo(21,'translate [2,0,0],ligands;')
cmd.mdo(22,'translate [2,0,0],ligands;')
cmd.mdo(23,'translate [2,0,0],ligands;')
cmd.mdo(24,'translate [2,0,0],ligands;')
cmd.mdo(25,'translate [2,0,0],ligands;')
cmd.mdo(26,'translate [2,0,0],ligands;')
cmd.mdo(27,'translate [2,0,0],ligands;')
cmd.mdo(28,'translate [2,0,0],ligands;')
cmd.mdo(29,'translate [2,0,0],ligands;')
cmd.mdo(30,'translate [2,0,0],ligands;')
cmd.mdo(31,'translate [2,0,0],ligands;')
cmd.mdo(32,'translate [2,0,0],ligands;')
cmd.mdo(33,'translate [2,0,0],ligands;')
cmd.mdo(34,'translate [2,0,0],ligands;')
cmd.mdo(35,'translate [2,0,0],ligands;')
cmd.mdo(36,'translate [2,0,0],ligands;')
cmd.mdo(37,'translate [2,0,0],ligands;')
cmd.mdo(38,'translate [2,0,0],ligands;')
cmd.mdo(39,'translate [2,0,0],ligands;')
cmd.mdo(40,'translate [2,0,0],ligands;')
cmd.mdo(41,'translate [2,0,0],ligands;')
cmd.mdo(42,'orient')
cmd.util.mroll('42','222','1')
cmd.mdo(223,'translate [-2,0,0],ligands;')
cmd.mdo(224,'translate [-2,0,0],ligands;')
cmd.mdo(225,'translate [-2,0,0],ligands;')
cmd.mdo(226,'translate [-2,0,0],ligands;')
cmd.mdo(227,'translate [-2,0,0],ligands;')
cmd.mdo(228,'translate [-2,0,0],ligands;')
cmd.mdo(229,'translate [-2,0,0],ligands;')
cmd.mdo(230,'translate [-2,0,0],ligands;')
cmd.mdo(231,'translate [-2,0,0],ligands;')
cmd.mdo(232,'translate [-2,0,0],ligands;')
cmd.mdo(233,'translate [-2,0,0],ligands;')
cmd.mdo(234,'translate [-2,0,0],ligands;')
cmd.mdo(235,'translate [-2,0,0],ligands;')
cmd.mdo(236,'translate [-2,0,0],ligands;')
cmd.mdo(237,'translate [-2,0,0],ligands;')
cmd.mdo(238,'translate [-2,0,0],ligands;')
cmd.mdo(239,'translate [-2,0,0],ligands;')
cmd.mdo(240,'translate [-2,0,0],ligands;')
cmd.mdo(241,'translate [-2,0,0],ligands;')
cmd.mdo(242,'translate [-2,0,0],ligands;')
cmd.mdo(243,'translate [-2,0,0],ligands;')
cmd.mdo(244,'translate [-2,0,0],ligands;')
cmd.mdo(245,'translate [-2,0,0],ligands;')
cmd.mdo(246,'translate [-2,0,0],ligands;')
cmd.mdo(247,'translate [-2,0,0],ligands;')
cmd.mdo(248,'translate [-2,0,0],ligands;')
cmd.mdo(249,'translate [-2,0,0],ligands;')
cmd.mdo(250,'translate [-2,0,0],ligands;')
cmd.mdo(251,'translate [-2,0,0],ligands;')
cmd.mdo(252,'translate [-2,0,0],ligands;')
cmd.mdo(253,'translate [-2,0,0],ligands;')
cmd.mdo(254,'translate [-2,0,0],ligands;')
cmd.mdo(255,'translate [-2,0,0],ligands;')
cmd.mdo(256,'translate [-2,0,0],ligands;')
cmd.mdo(257,'translate [-2,0,0],ligands;')
cmd.mdo(258,'translate [-2,0,0],ligands;')
cmd.mdo(259,'translate [-2,0,0],ligands;')
cmd.mdo(260,'translate [-2,0,0],ligands;')
cmd.mdo(261,'translate [-2,0,0],ligands;')
cmd.mdo(262,'translate [-2,0,0],ligands;')
cmd.mdo(263,'orient')
cmd.util.mroll('264','442','1')
else:
showinfo('No ligands','There are no ligands in this PDB.')
def reps(self, cleanup=0):
rep_list = [
"lines", "sticks", "spheres", "surface", "mesh", "dots", "ribbon",
"cartoon"
]
try:
if not cleanup:
cmd.disable()
cmd.set("suspend_updates", 1, quiet=1)
cmd.load("$PYMOL_DATA/demo/pept.pdb", "rep1")
cmd.alter("rep1///1-5+8-13/", "ss='S'")
cmd.cartoon("auto")
cmd.hide("everything", "rep1")
for a in range(2, 9):
cmd.create("rep%d" % a, "rep1")
for x, y in enumerate(rep_list, 1):
cmd.show(x, "rep%d" % y)
cmd.reset()
cmd.zoom("rep1", 24)
util.cbay("rep2")
util.cbac("rep3")
util.cbas("rep4")
util.cbab("rep5")
util.cbaw("rep6")
util.cbay("rep8")
cmd.set("suspend_updates", 0, quiet=1)
scale = 0.5
for b in range(1, 20):
cmd.set("suspend_updates", 0, quiet=1)
cmd.refresh()
cmd.set("suspend_updates", 1, quiet=1)
xt = -3.2
yt = 1.6
for a in range(1, 5):
cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
yt = -yt
xt = -3.2
for a in range(5, 9):
cmd.translate([xt * scale, yt * scale, 0],
object="rep%d" % a,
camera=0)
xt = xt + 2
for a in range(1, 9):
cmd.origin("rep%d" % a, object="rep%d" % a)
cmd.mset("1")
st = ' '.join(
map(
lambda x, y: "rotate angle=-3,object=rep%d,axis=%s;" %
(x, y), list(range(1, 9)),
['x', 'y', 'x', 'y', 'x', 'y', 'x', 'y']))
cmd.mdo(1, st)
cmd.set("suspend_updates", 0, quiet=1)
cmd.mplay()
cgo = []
axes = [[4.5, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]]
c = 1
for a in rep_list:
ext = cmd.get_extent("rep%d" % c)
pos = [(ext[0][0] + ext[1][0]) / 2,
(ext[0][1] + ext[1][1]) / 2 + 14,
(ext[0][2] + ext[1][2]) / 2]
c = c + 1
pos[0] = pos[0] - (measure_text(plain, a, axes) / 2)
wire_text(cgo, plain, pos, a, axes)
cmd.set("cgo_line_width", 1.5)
cmd.set("auto_zoom", 0)
cmd.load_cgo(cgo, 'reps')
cmd.set("auto_zoom", 1)
else:
cmd.delete("rep*")
cmd.mset()
cmd.mstop()
except:
traceback.print_exc()
def reps(self,cleanup=0):
rep_list = [ "lines","sticks","spheres","surface","mesh","dots","ribbon","cartoon" ]
try:
if not cleanup:
cmd.disable()
cmd.set("suspend_updates",1,quiet=1)
cmd.load("$PYMOL_DATA/demo/pept.pdb","rep1")
cmd.alter("rep1///1-5+8-13/","ss='S'")
cmd.cartoon("auto")
cmd.hide("everything","rep1")
for a in range(2,9):
cmd.create("rep%d"%a,"rep1")
for x, y in enumerate(rep_list, 1):
cmd.show(x, "rep%d" % y)
cmd.reset()
cmd.zoom("rep1",24)
util.cbay("rep2")
util.cbac("rep3")
util.cbas("rep4")
util.cbab("rep5")
util.cbaw("rep6")
util.cbay("rep8")
cmd.set("suspend_updates",0,quiet=1)
scale=0.5
for b in range(1,20):
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.set("suspend_updates",1,quiet=1)
xt=-3.2
yt=1.6
for a in range(1,5):
cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
xt=xt+2
yt=-yt
xt=-3.2
for a in range(5,9):
cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
xt=xt+2
for a in range(1,9):
cmd.origin("rep%d"%a,object="rep%d"%a)
cmd.mset("1")
st = ' '.join(map(lambda x,y:"rotate angle=-3,object=rep%d,axis=%s;"%(x,y),list(range(1,9)),
['x','y','x','y','x','y','x','y']))
cmd.mdo(1,st)
cmd.set("suspend_updates",0,quiet=1)
cmd.mplay()
cgo = []
axes = [[4.5,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]]
c = 1
for a in rep_list:
ext = cmd.get_extent("rep%d"%c)
pos = [(ext[0][0]+ext[1][0])/2,
(ext[0][1]+ext[1][1])/2+14,
(ext[0][2]+ext[1][2])/2]
c = c + 1
pos[0]=pos[0]-(measure_text(plain,a,axes)/2)
wire_text(cgo,plain,pos,a,axes)
cmd.set("cgo_line_width",1.5)
cmd.set("auto_zoom",0)
cmd.load_cgo(cgo,'reps')
cmd.set("auto_zoom",1)
else:
cmd.delete("rep*")
cmd.mset()
cmd.mstop()
except:
traceback.print_exc()
def stop():
cmd.mstop()
def surface_stick():
'''surface over stick movie'''
glb.update()
cmd.mstop()
cmd.mclear()
cmd.mset()
cmd.mset('1', '60')
glb.procolor(None,show_all=('sticks','surface'))
cmd.mdo(1,'set transparency = 0.75, all;')
cmd.mdo(2,'set transparency = 0.7, all;')
cmd.mdo(3,'set transparency = 0.65, all;')
cmd.mdo(4,'set transparency = 0.6, all;')
cmd.mdo(5,'set transparency = 0.55, all;')
cmd.mdo(6,'set transparency = 0.5, all;')
cmd.mdo(7,'set transparency = 0.45, all;')
cmd.mdo(8,'set transparency = 0.4, all;')
cmd.mdo(9,'set transparency = 0.35, all;')
cmd.mdo(10,'set transparency = 0.3, all;')
cmd.mdo(11,'set transparency = 0.25, all;')
cmd.mdo(12,'set transparency = 0.2, all;')
cmd.mdo(13,'set transparency = 0.15, all;')
cmd.mdo(14,'set transparency = 0.1, all;')
cmd.mdo(15,'set transparency = 0.05, all;')
cmd.mdo(16,'set transparency = 0, all;')
cmd.mdo(17,'set transparency = 0, all;')
cmd.mdo(19,'set transparency = 0, all;')
cmd.mdo(20,'set transparency = 0, all;')
cmd.mdo(21,'set transparency = 0, all;')
cmd.mdo(22,'set transparency = 0, all;')
cmd.mdo(23,'set transparency = 0, all;')
cmd.mdo(24,'set transparency = 0, all;')
cmd.mdo(25,'set transparency = 0, all;')
cmd.mdo(26,'set transparency = 0, all;')
cmd.mdo(27,'set transparency = 0, all;')
cmd.mdo(28,'set transparency = 0, all;')
cmd.mdo(29,'set transparency = 0.05, all;')
cmd.mdo(30,'set transparency = 0.1, all;')
cmd.mdo(31,'set transparency = 0.15, all;')
cmd.mdo(32,'set transparency = 0.2, all;')
cmd.mdo(33,'set transparency = 0.25, all;')
cmd.mdo(34,'set transparency = 0.3, all;')
cmd.mdo(35,'set transparency = 0.35, all;')
cmd.mdo(36,'set transparency = 0.4, all;')
cmd.mdo(37,'set transparency = 0.45, all;')
cmd.mdo(38,'set transparency = 0.5, all;')
cmd.mdo(39,'set transparency = 0.55, all;')
cmd.mdo(40,'set transparency = 0.6, all;')
cmd.mdo(41,'set transparency = 0.65, all;')
cmd.mdo(42,'set transparency = 0.7, all;')
cmd.mdo(43,'set transparency = 0.75, all;')
cmd.mdo(44,'set transparency = 0.8, all;')
cmd.mdo(45,'set transparency = 0.85, all;')
cmd.mdo(46,'set transparency = 0.9, all;')
cmd.mdo(47,'set transparency = 0.9, all;')
cmd.mdo(48,'set transparency = 0.9, all;')
cmd.mdo(49,'set transparency = 0.85, all;')
cmd.mdo(50,'set transparency = 0.85, all;')
cmd.mdo(51,'set transparency = 0.85, all;')
cmd.mdo(52,'set transparency = 0.85, all;')
cmd.mdo(53,'set transparency = 0.85, all;')
cmd.mdo(54,'set transparency = 0.85, all;')
cmd.mdo(55,'set transparency = 0.85, all;')
cmd.mdo(56,'set transparency = 0.85, all;')
cmd.mdo(57,'set transparency = 0.85, all;')
cmd.mdo(58,'set transparency = 0.85, all;')
cmd.mdo(59,'set transparency = 0.85, all;')
cmd.mdo(60,'set transparency = 0.8, all;')
def growProtein():
cmd.mstop()
cmd.mclear()
cmd.mset()
glb.update()
objects = cmd.get_names('all')
if 'protein' in objects:
cmd.bg_color('black')
# create the objects to be used in this movie
cmd.create('helix', 'ss h and protein')
cmd.create('sheets', 'ss s and protein')
cmd.create('surface', objects[0])
cmd.mset('1', '1400')
# dna and rna will be represented as sticks
# to make them stand out from the protein
if 'dna' in objects:
glb.procolor('dna','sticks','cpk',None)
if 'rna' in objects:
glb.procolor('rna','sticks','cpk',None)
# coloring the protein and secondary structures
cmd.color('white', 'protein')
cmd.color('purple', 'helix')
cmd.color('teal', 'sheets')
cmd.cartoon('loop', 'protein')
cmd.cartoon('automatic', 'helix')
cmd.cartoon('automatic', 'sheets')
cmd.hide('all')
cmd.show('cartoon', 'protein')
#cmd.mdo(1,'hide cartoon, helix; hide cartoon, sheets;')
cmd.util.mrock('2', '200', '90', '1', '1')
cmd.mdo(201,'show cartoon, helix;')
cmd.util.mrock('202', '400', '90', '1', '1')
cmd.mdo(401,'show cartoon, sheets;')
cmd.util.mrock('402', '600', '90', '1', '1')
if 'ligands' in objects:
cmd.color('hotpink', 'ligands')
cmd.mdo(600, 'show spheres, ligands; show sticks, ligands;'+
' set sphere_transparency = 0.5, ligands;')
cmd.util.mroll('601', '800', '1', axis = "x")
cmd.color('blue', 'surface')
cmd.mview('store', '800')
cmd.turn('z', 180)
cmd.mview('store' , '1000')
cmd.turn('z', 180)
cmd.mdo(800, 'show surface, surface; '+
'set transparency = 0.8, surface;')
cmd.mdo(850,'set transparency = 0.7, surface;')
cmd.mdo(900,'set transparency = 0.6, surface;')
cmd.mdo(950,'set transparency = 0.5, surface;')
cmd.mdo(1000,'set transparency = 0.4, surface;')
cmd.mdo(1050,'set transparency = 0.3, surface;')
cmd.mdo(1100,'set transparency = 0.2, surface;')
cmd.mdo(1150,'set transparency = 0.1, surface;')
cmd.mdo(1200,'set transparency = 0.0, surface;')
cmd.mview('store', '1200')
cmd.util.mrock('1201', '1399', '180', '1', '1')
cmd.hide('everything', 'surface')
cmd.hide('everything', 'helix')
cmd.hide('everything', 'sheets')
cmd.reset()
cmd.orient()
cmd.mdo(1400,'hide everything, all; show cartoon, protein;')
cmd.mdo(1400,'mstop')
cmd.mview('interpolate')
cmd.rewind()
def rewind():
cmd.mstop()
cmd.rewind()
