def bond_connections_from_array(interactiongraph, residuemap, cutoff=0.0):
# Make strength be proportional to girth of bonds
graph = numpy.sqrt(numpy.absolute(interactiongraph))
# Simple min-max scaling parameters
minimum = numpy.min(graph)
maximum = numpy.max(graph)
residues = list(residuemap.keys())
shown = []
for i in range(graph.shape[0]):
for j in range(i, graph.shape[1]):
# Only draw bonds if interaction strength over cutoff threshold
if graph[i][j] > cutoff:
resa = residues[i]
resb = residues[j]
shown.append(resa)
shown.append(resb)
a = "chain {} and resi {} and name CA".format(
resa.split(':')[0],
resa.split(':')[1][1:])
b = "chain {} and resi {} and name CA".format(
resb.split(':')[0],
resb.split(':')[1][1:])
cmd.bond(a, b)
strength = 1.0 if maximum == minimum else 0.1 + (0.9 * (
(graph[i][j] - minimum) / (maximum - minimum)))
cmd.set_bond("stick_radius", strength, a, b)
return shown
def bond_connections(clusters, interactions):
cutoff=10
## show_list=["A:240","A:182","A:184","A:204","A:201","A:216"]
# shell1=["A:240"]
## shell1=["A:204","A:240"]
# shell2=["A:182","A:184","A:204","A:201","A:216"]
# shell3=["A:151","A:155","A:156","A:199","A:205","A:208","A:214","A:238","A:242"]
# shell4=["A:154","A:158","A:163","A:166","A:167","A:170","A:180","A:185","A:196","A:203","A:207","A:211","A:212","A:219","A:68"]
# shell5=["A:135","A:136","A:149","A:160","A:162","A:164","A:171","A:173","A:174","A:178","A:192","A:197","A:200","A:206","A:222","A:230","A:235","A:236","A:237","A:26","A:29","A:66","A:69"]
# shell6=["A:134","A:138","A:139","A:143","A:146","A:152","A:157","A:159","A:169","A:183","A:187","A:19","A:195","A:220","A:223","A:227","A:23","A:232","A:24","A:244","A:46","A:87","A:89","A:90","A:91"]
#
# show_list_wt=shell1 + shell2 + shell3 + shell4 + shell5 + shell6
# show_list_S=shell1
# show_list=shell1
# #show_list=show_list_wt
# #show_list.append(shell1)
# #show_list.append(shell2)
# #print(show_list)
for cluster in clusters:
#print(cluster)
for i in range(len(cluster)):
for j in range(i, len(cluster)):
resa = cluster[i]
resb = cluster[j]
# Only draw bonds if interaction strength at all present
if resa in interactions:
if resb in interactions[resa]:
resa_=re.sub(r':\w',':',resa)
resb_=re.sub(r':\w',':',resb)
a = "chain {} and resi {} and name CA".format(
resa_.split(':')[0], resa_.split(':')[1])
b = "chain {} and resi {} and name CA".format(
resb_.split(':')[0], resb_.split(':')[1])
# if interactions[resa][resb] > cutoff and (resa in show_list or resb in show_list):
if interactions[resa][resb] > cutoff: #and (resa in show_list or resb in show_list):
#if resa not in show_list:
# print(resa)
#if resb not in show_list:
# print(resb)
# print(resa + " " + resb)
print(a + " " + b + " " + str(interactions[resa][resb]))
cmd.bond(a, b)
cmd.set_bond("line_width",
(interactions[resa][resb]/3),
a, b)
cmd.set_bond("line_color",get_color(resa,resb),a,b)
def display_graphkernel(pdb_id, pdb_path):
'''
'''
# Load PDB
cmd.bg_color('white')
cmd.load(pdb_path + pdb_id[:-2] + '.pdb')
cmd.split_chains(pdb_id[:-2])
for name in cmd.get_names('objects', 0, '(all)'):
if not name.endswith(pdb_id[-1].upper()) and name.startswith(
pdb_id[:4]):
cmd.delete(name)
else:
zero_residues(name)
cmd.reset()
pdb_id2 = pdb_id + 'copy'
cmd.create(pdb_id2, pdb_id)
cmd.hide('everything', pdb_id)
cmd.show_as('lines', pdb_id + ' and (name ca or name c or name n)')
cmd.set('line_width', 5)
cmd.set_bond('line_width', 5,
pdb_id + ' and (name ca or name c or name n)')
cmd.show('spheres', pdb_id + ' and name ca')
cmd.set('sphere_transparency', 0.0, pdb_id + ' and name ca')
cmd.set('sphere_scale', 0.5, pdb_id + ' and name ca')
cmd.hide('everything', pdb_id2)
cmd.show('spheres', pdb_id2 + ' and name ca')
cmd.set('sphere_transparency', 0.8, pdb_id2 + ' and name ca')
cmd.set('sphere_scale', code2[elem], elem + '&' + selection)
#cmd.set('sphere_scale', 2, pdb_id2 + ' and name ca')
data = cmd.get_coords(selection=pdb_id + ' and name ca', state=1)
j = 55
cmd.set('dash_width', 1.0)
cmd.set('dash_color', 'marine')
for i in range(len(data)):
cmd.distance('d' + str(i) + str(j),
pdb_id2 + ' and name ca and res ' + str(i),
pdb_id2 + ' and name ca and res ' + str(j))
cmd.hide('labels', 'd' + str(i) + str(j))
resicolor(pdb_id)
resicolor(pdb_id)
resicolor(pdb_id2, True)
def load_network(points, edges):
with open(points, 'r') as infile:
for line in infile.readlines():
field = line.strip().split()
xyz = map(float, field)
xyz = [10 * x for x in xyz]
cmd.pseudoatom("test", elem='O', pos=xyz)
with open(edges, 'r') as infile:
for line in infile.readlines():
field = line.strip().split()
if float(field[-1]) > 0.1:
plop = cmd.bond('index %s' % field[0], 'index %s' % field[1])
cmd.set_bond('line_color', float(field[-1]), 'i. 1')
cmd.show("sphere", "test")
cmd.set('line_width', 5.0)
return 0
def bond_connections(clusters, interactions):
# Quickfix - find min and max
# this filtering should be done before supplying to this function
# That is, the "interactions" data should be already formatted
# as a float in a way that makes it look nice with bond
# stick_radius
minimum = None
maximum = None
for cluster in clusters:
for i in range(len(cluster)):
for j in range(i, len(cluster)):
resa = cluster[i]
resb = cluster[j]
if resa in interactions:
if resb in interactions[resa]:
strength = interactions[resa][resb][0]
if minimum is None:
minimum = strength
else:
minimum = strength if minimum > strength else minimum
if maximum is None:
maximum = strength
else:
maximum = strength if maximum < strength else maximum
for cluster in clusters:
for i in range(len(cluster)):
for j in range(i, len(cluster)):
resa = cluster[i]
resb = cluster[j]
# Only draw bonds if interaction strength at all present
if resa in interactions:
if resb in interactions[resa]:
a = "chain {} and resi {} and name CA".format(
resa.split(':')[0],
resa.split(':')[1][1:])
b = "chain {} and resi {} and name CA".format(
resb.split(':')[0],
resb.split(':')[1][1:])
cmd.bond(a, b)
strength = 1.0 if maximum == minimum else 0.1 + (
0.9 * ((interactions[resa][resb][0] - minimum) /
(maximum - minimum)))
cmd.set_bond("stick_radius", strength, a, b)
def bond_colors_from_array(colorarray,
residuemap,
cutoff=0.0,
colorprefix="path_"):
residues = list(residuemap.keys())
colored = []
colors = {}
colorindex = 0
numcolors = 0
# Expect rgb channels over first dimension
for i in range(colorarray.shape[1]):
for j in range(i, colorarray.shape[2]):
# Only draw bonds if interaction strength over cutoff threshold
resa = residues[i]
resb = residues[j]
colored.append((resa, resb))
a = "chain {} and resi {} and name CA".format(
resa.split(':')[0],
resa.split(':')[1][1:])
b = "chain {} and resi {} and name CA".format(
resb.split(':')[0],
resb.split(':')[1][1:])
#cmd.bond(a, b)
color = tuple(colorarray[0:3, i, j])
if color not in colors:
colorindex = numcolors + 1
numcolors += 1
colors[color] = colorindex
cmd.set_color("{}{}".format(colorprefix, colorindex), color)
else:
colorindex = colors[color]
colorname = "{}{}".format(colorprefix, colorindex)
print("Applying color {}, named as {}, to residues {}".format(
color, colorname, colored[-1]))
cmd.set_bond("stick_color", colorname, a, b)
print(colors)
return colored, colors
def zoom_around(self, near=5, zoom=4):
from pymol import cmd
cmd.hide()
sele = self.selector()
tgt = '{} and ! name c+n+o+h'.format(sele)
cmd.set_bond('stick_color', 'white', sele)
cmd.set_bond('stick_radius', 0.14, sele)
cmd.set('sphere_scale', 0.25, sele)
cmd.show('sticks', tgt)
cmd.show('spheres', tgt)
cmd.select('rz-target', sele)
cmd.select('rz-around', 'byres {} around {}'.format(sele, near))
cmd.deselect()
cmd.show('(byres {} around {}) and ! name c+n+o+h'.format(sele, near))
cmd.show('////HOH')
cmd.show('ribbon', 'byres {} expand {}'.format(sele, near))
cmd.orient(sele)
cmd.zoom(sele, zoom)
from pymol import cmd
cmd.bg_color('white')
cmd.select('drg', 'all')
cmd.set('valence', 1)
cmd.set_bond('stick_radius', '0.14', 'drg', 'drg')
cmd.set('sphere_scale', '0.25', 'drg')
cmd.show('sticks', 'drg')
cmd.show('spheres', 'drg')
# output
cmd.set('antialias', '2')
cmd.set('direct', '0.6')
cmd.set('orthoscopic', 'on')
cmd.set('ray_trace_frames', '1')
#cmd.ray(renderer=-1)
#cmd.png('~/Downloads/charge.png', dpi=600)
cmd.load('_xyzfile.xyz')
#cmd.bond('id 1', 'id 2')
#cmd.bond('id 1', 'id 3')
#cmd.bond('id 1', 'id 4')
#cmd.set_bond ('stick_color', 'white', 'all', 'all')
#cmd.set_bond ('stick_radius', -0.14, 'all', 'all')
#cmd.set ('stick_ball', 1)
#cmd.set ('stick_ball_ratio', -1)
#cmd.set ('stick_ball_color', 'atomic')
#cmd.show ('sticks', 'all')
#cmd.color('black', 'id 1')
#cmd.color('gray', '(name Au*)')
cmd.set_bond('stick_radius', 0.1, 'all', 'all')
cmd.set('sphere_scale', 0.15, 'all')
cmd.show('sticks', 'all')
cmd.show('spheres', 'all')
cmd.set('stick_ball_color', 'atomic')
cmd.color('gray20', '(name C*)')
cmd.set('transparency_mode', 1)
#w = 0.01 # cylinder width
#l = 0.5 # cylinder length
#h = 0.15 # cone hight
#d = w * 1.618 # cone base diameter
w = 0.03 # cylinder width
l = 1.65 # cylinder length
def display_graphpool(pdb_id, pdb_path):
'''
'''
# Load PDB
cmd.bg_color('white')
cmd.load(pdb_path + pdb_id[:-2] + '.pdb')
cmd.split_chains(pdb_id[:-2])
for name in cmd.get_names('objects', 0, '(all)'):
if not name.endswith(pdb_id[-1].upper()) and name.startswith(
pdb_id[:4]):
cmd.delete(name)
else:
zero_residues(name)
cmd.reset()
pdb_id2 = pdb_id + 'copy'
cmd.create(pdb_id2, pdb_id)
cmd.color('grey', pdb_id)
cmd.hide('everything', pdb_id)
cmd.show_as('lines', pdb_id + ' and (name ca)')
cmd.set('line_width', 5)
cmd.set_bond('line_width', 5, pdb_id + ' and (name ca)')
cmd.show('spheres', pdb_id + ' and name ca')
cmd.set('sphere_transparency', 0.0, pdb_id + ' and name ca')
cmd.set('sphere_scale', 0.5, pdb_id + ' and name ca')
data = cmd.get_coords(selection=pdb_id + ' and name ca', state=1)
data_ = []
cmd.set('dash_color', 'marine')
cmd.set('dash_width', 1.0)
j = 55
for i in range(len(data)):
if i % 2 == 0 and i + 1 < len(data):
data[i] = np.mean(data[i:i + 2], axis=0)
data[i + 1] = np.array([10000, 10000, 10000])
#cmd.distance('d'+str(i)+str(j), pdb_id + ' and name ca and res ' + str(i), pdb_id + ' and name ca and res ' + str(j))
#cmd.hide('labels', 'd'+str(i)+str(j))
cmd.color('red', pdb_id2)
cmd.hide('everything', pdb_id2)
cmd.show_as('lines', pdb_id2 + ' and (name ca)')
cmd.set('line_width', 5)
cmd.set_bond('line_width', 5, pdb_id2 + ' and (name ca)')
cmd.show('spheres', pdb_id2 + ' and name ca')
cmd.set('sphere_transparency', 0.0, pdb_id2 + ' and name ca')
cmd.set('sphere_scale', 0.5, pdb_id2 + ' and name ca')
for i in range(len(data)):
if i % 2 == 0 and i + 1 < len(data):
cmd.alter_state(1, pdb_id2 + ' and name ca and res ' + str(i),
'(x,y,z)=' + str(tuple(data[i])))
else:
cmd.hide('spheres', pdb_id2 + ' and name ca and res ' + str(i))
pdb_id3 = pdb_id + 'copy2'
cmd.create(pdb_id3, pdb_id2)
cmd.color('red', pdb_id3)
cmd.hide('everything', pdb_id3)
cmd.show_as('lines', pdb_id3 + ' and (name ca)')
cmd.set('line_width', 5)
cmd.set_bond('line_width', 5, pdb_id3 + ' and (name ca)')
cmd.show('spheres', pdb_id3 + ' and name ca')
cmd.set('sphere_transparency', 0.8, pdb_id3 + ' and name ca')
for i in range(len(data)):
if i % 2 == 0 and i + 1 < len(data):
cmd.set('sphere_scale', np.random.uniform(1.0, 4.5),
pdb_id3 + ' and name ca and res ' + str(i))
else:
cmd.hide('spheres', pdb_id2 + ' and name ca and res ' + str(i))
def testSetBond(self):
value = 2.3
cmd.fragment('ala')
cmd.set_bond('stick_radius', value, '*', '*')
v_list = cmd.get_bond('stick_radius', 'first *', '*')
self.assertAlmostEqual(v_list[0][1][0][2], value)
A = AggregatTransferFromFile(fname)
cmd.set_view ([
-0.480811268, 0.603387773, 0.636203885,
0.675508440, 0.717507422, -0.169974893,
-0.559037924, 0.348030269, -0.752567112,
-0.000127681, 0.000030167, -122.974456787,
13.921709061, -7.469791889, -4.264435768,
-1086.176879883, 1332.132446289, -20.000000000])
# select only a few sample points
indices = [0, 250, 500, 1000, 1999]
t = np.linspace(0, A._tLength, A._tSteps)[indices]
# Get values ordered by time in first index
values = np.swapaxes(A.get(), 0, 1)[indices]
selections = ['lab{}'.format(i + 1) for i in range(8)]
for lab in selections:
cmd.label(lab, '')
selections = ['bcl{}'.format(i + 1) for i in range(7)]
for i, val in enumerate(values):
alpha = p_to_alpha(val)
for n, bcl in enumerate(selections):
cmd.set_bond('stick_transparency', alpha[n], bcl)
cmd.refresh()
cmd.ray(width, height)
print('Belongs to time {}'.format(t[i] * 5.20883746))
cmd.png('../fmo_transfer_{}.png'.format(i), dpi=DPI, ray=1)
def testSetBond(self):
value = 2.3
cmd.fragment('ala')
cmd.set_bond('stick_radius', value, '*', '*')
v_list = cmd.get_bond('stick_radius', 'first *', '*')
self.assertAlmostEqual(v_list[0][1][0][2], value)
cmd.bond("/1-tess/pro/A/71/OE2", "/1-tess/lig/0/0/O6")
cmd.bond("/1-tess/pro/A/71/OE2", "/1-tess/lig/0/0/C8")
cmd.bond("/1-tess/pro/A/71/OE2", "/1-tess/lig/0/0/C9")
cmd.bond("/1-tess/pro/A/71/OE2", "/1-tess/lig/0/0/C10")
cmd.bond("/1-tess/pro/A/71/OE2", "/1-tess/lig/0/0/O9")
cmd.bond("/1-tess/pro/A/71/OE2", "/1-tess/lig/0/0/O10")
cmd.bond("/1-tess/pro/A/71/OE2", "/1-tess/lig/0/0/O11")
cmd.bond("/1-tess/pro/A/73/CD", "/1-tess/lig/0/0/O8")
cmd.bond("/1-tess/pro/A/73/NE", "/1-tess/lig/0/0/O8")
cmd.bond("/1-tess/pro/A/73/CZ", "/1-tess/lig/0/0/O8")
cmd.bond("/1-tess/pro/A/73/NH1", "/1-tess/lig/0/0/O7")
cmd.bond("/1-tess/pro/A/73/NH1", "/1-tess/lig/0/0/O8")
cmd.bond("/1-tess/pro/A/73/NH2", "/1-tess/lig/0/0/O8")
cmd.bond("/1-tess/pro/A/73/NH2", "/1-tess/lig/0/0/O9")
cmd.bond("/1-tess/pro/A/123/OD2", "/1-tess/lig/0/0/O3")
cmd.set_bond("line_color", "forest", "1-tess")
cmd.set_bond("line_width", 0.25, "1-tess")
cmd.bond("/1-tess/pro/A/29/OG", "/1-tess/pro/A/31/CG2")
cmd.bond("/1-tess/pro/A/29/OG", "/1-tess/pro/A/46/OD1")
cmd.bond("/1-tess/pro/A/29/OG", "/1-tess/pro/A/52/CE1")
cmd.bond("/1-tess/pro/A/29/OG", "/1-tess/pro/A/123/OD2")
cmd.bond("/1-tess/pro/A/31/CG2", "/1-tess/pro/A/44/CE1")
cmd.bond("/1-tess/pro/A/31/CG2", "/1-tess/pro/A/46/OD1")
cmd.bond("/1-tess/pro/A/31/CG2", "/1-tess/pro/A/123/OD2")
cmd.bond("/1-tess/pro/A/33/ND2", "/1-tess/pro/A/44/CE1")
cmd.bond("/1-tess/pro/A/33/ND2", "/1-tess/pro/A/63/NZ")
cmd.bond("/1-tess/pro/A/33/ND2", "/1-tess/pro/A/68/CZ2")
cmd.bond("/1-tess/pro/A/33/ND2", "/1-tess/pro/A/123/OD2")
cmd.bond("/1-tess/pro/A/44/CD2", "/1-tess/pro/A/44/NE2")
cmd.bond("/1-tess/pro/A/44/CD2", "/1-tess/pro/A/59/CG1")
cmd.bond("/1-tess/pro/A/44/CD2", "/1-tess/pro/A/61/CB")
if current_m != last_m or current_p != last_p:
last_m = current_m
last_p = current_p
try:
cmd.delete('my_map.2fofc')
cmd.delete('my_map.fofc')
cmd.load(pdbFile, 'overall_best')
cmd.load_mtz(reflectionFile, prefix='my_map'
) #, amplitudes = 'unknown/unknown291019/REFM_FWT',
#phases = 'unknown/unknown291019/REFM_PHWT',reso_low = 23.96, reso_high = 1.9)
#cmd.map_double("my_map")
cmd.map_double("my_map.2fofc")
print("upload finished")
cmd.hide("everything")
cmd.show("sticks")
cmd.set_bond('stick_radius', '0.1', 'overall_best')
cmd.center()
cmd.select('site',
'br. all within ' + str(radius_check) + ' of center')
cmd.isomesh('map', 'my_map.2fofc', 1.0, 'site', carve=1.6)
cmd.color('gray40', 'map')
cmd.set('mesh_width', '0.1')
cmd.bg_color('white')
cmd.set("ray_trace_fog", "0")
from pymol import cmd
cmd.bg_color('white')
cmd.select('drg', 'all')
cmd.set('valence', '1')
cmd.set_bond('stick_radius', '0.14', 'drg', 'drg')
cmd.set('sphere_scale', '0.25', 'drg')
cmd.show('sticks', 'drg')
cmd.show('spheres', 'drg')
cmd.set_view ([0.987891138, -0.139472052, -0.067891687,
0.152521998, 0.793636620, 0.588958621,
-0.028259384, -0.592185259, 0.805302858,
0.000017954, 0.000006792, -52.386489868,
-1.638074398, -1.409737468, -0.143483341,
-34.060420990, 138.833740234, 20.000000000])
charges = ["-0.103" ," 0.115" ," 0.016" ,"-0.082" ," 0.068" ,"-0.022" ,"-0.017" ," 0.017" ,"-0.001" ,"-0.051" ," 0.120" ,"-0.186" ," 0.163" ,"-0.115" ," 0.216" ,"-0.142" ," 0.130" ,"-0.294" ," 0.114" ,"-0.004" ," 0.102" ,"-0.098" ,"-0.004" ," 0.102" ,"-0.294" ," 0.114" ," 0.882" ,"-0.582" ,"-0.582" ,"-0.582"]
cmd.set('label_size', '22')
cmd.set('label_position', (0, 2, 2))
for i, charge in zip(range(1, 31), charges):
cmd.label('id %s' % i, charge)
# output
cmd.set('antialias', '2')
cmd.set('direct', '0.6')
cmd.set('orthoscopic', 'on')
cmd.set('ray_trace_frames', '1')
#cmd.ray(renderer=-1)
#cmd.png('~/Downloads/charge.png', dpi=600)
def visualize_path((path, freq, pdb, outfile)):
nodes = path.split('=>')
save_pse = True
#print outfile
#print freq
#sys.exit()
#print nodes
node_color = sns.color_palette("Reds", n_colors=len(nodes))
node_color.reverse()
#print node_color
cmd.reinitialize()
cmd.load(pdb)
cmd.hide("everything")
# cmd.show("ribbon")
cmd.show("cartoon")
#resa = re.sub(r':\w', ':', nodes[0])
(chain, resnum) = re.split(':\w', nodes[0])
a = "chain {} and resi {} and name CA".format(chain, resnum)
cmd.show("spheres", a)
colorname = "color" + str(0)
cmd.set_color(colorname, node_color[0])
cmd.color(colorname, a)
cmd.label(a, '" %s:%s" % (resi, resn)')
cmd.set("label_color", "red", a)
#cmd.label(a, '"%s" % (resi)')
for i in range(1, len(nodes)):
#resb = re.sub(r':\w', ':', nodes[i])
(chain, resnum) = re.split(':\w', nodes[i])
b = "chain {} and resi {} and name CA".format(chain, resnum)
#print a,b
cmd.bond(a, b)
cmd.set_bond("line_width", 5, a, b)
cmd.set_bond("line_color", "red", a, b)
cmd.show("lines", a)
cmd.show("spheres", a)
cmd.show("lines", b)
cmd.show("spheres", b)
colorname = "color" + str(i)
cmd.set_color(colorname, node_color[i])
cmd.color(colorname, b)
#cmd.label(b,'" %s:%s" % (resi, resn)')
cmd.label(b, '" %s%s" % (one_letter[resn],resi)')
#cmd.label(b, '"%s" % (resi)')
a = b
#cmd.color(node_color[len)],b)
#cmd.space("cmyk")
cmd.set("ray_shadow", "off")
#cmd.bg_color("white")
#cmd.label_position([3,2,1])
cmd.set("label_position", (2, 2, 2))
sele = "chain A and resi 131 and not name H*"
cmd.show("sticks", sele)
norm_factor = freq[nodes[0]]
node_freqs = {k: freq[k] for k in nodes}
#print node_freqs
#print freq[nodes]
#print sorted(node_freqs.values())
node_freq_min = min(node_freqs.values())
#print node_freq_min
#sys.exit()
scale_cutoff = min(0.25, min(node_freqs.values()) / norm_factor)
#print nodes
#print node_freqs
#print freq
#sys.exit()
for res in freq.keys():
scale = freq[res] / norm_factor
#print res,freq[res],scale,scale_cutoff
if scale > scale_cutoff:
(chain, resnum) = re.split(':\w', res)
sele = "chain {} and resi {} and name CA".format(chain, resnum)
cmd.show("spheres", sele)
cmd.set("sphere_scale", scale, selection=sele)
if not res in nodes: #give residue not on highest freq path a different color
last_color = len(nodes) - 1
#colorname="color"+str(last_color)
colorname = "grey60" #color" + str(last_color)
cmd.color(colorname, sele)
cmd.label(sele, '" %s%s" % (one_letter[resn],resi)')
cmd.util.cnc(sele)
#cmd.center("chain A")
cmd.deselect()
### cut below here and paste into script ###
cmd.set_view([\
0.354133159, -0.915425777, 0.191264138,\
-0.626513124, -0.384070098, -0.678214610,\
0.694314659, 0.120348796, -0.709537089,\
-0.000188543, -0.000061929, -119.472831726,\
33.501632690, 81.432159424, 143.041992188,\
87.118530273, 151.834289551, -20.000000000\
])
### cut above here and paste into script ###
#outfile="{}cluster{}-{}.png".format(outfolder,cut,freq)
# if ray:
# cmd.ray()
# cmd.sync(10)
cmd.save(outfile)
cmd.sync(10)
if save_pse:
outfile_pse = re.sub('.png', '.pse', outfile)
cmd.save(outfile_pse)
cmd.sync(10)