def colorbyB(selection="spheres",first=7,last=3): # Author: Scott Dixon
cols = [(0.,0.,1.),(.5,.5,1.),(.8,.8,1.),(1.,1.,1.),
(1.,.9,.9),(1.,.6,.6),(1.,0.,0.)]
nbins = len(cols)
incr = float(first-last)/nbins
for i in range(nbins):
cname = "_spcol%03d"%i
cmd.set_color(cname,cols[i])
b = first - i*incr
cmd.color(cname,"((%s) and not(b > %f) and b > %f)"%(selection,b,b-incr))
def colorbyB(selection="spheres", first=7, last=3): # Author: Scott Dixon
cols = [(0., 0., 1.), (.5, .5, 1.), (.8, .8, 1.), (1., 1., 1.),
(1., .9, .9), (1., .6, .6), (1., 0., 0.)]
nbins = len(cols)
incr = float(first - last) / nbins
for i in range(nbins):
cname = "_spcol%03d" % i
cmd.set_color(cname, cols[i])
b = first - i * incr
cmd.color(
cname,
"((%s) and not(b > %f) and b > %f)" % (selection, b, b - incr))
def rainbow(selection="(name ca and alt '',A)",reverse=0,_self=cmd):
pymol=_self._pymol
cmd=_self # NOT THREAD SAFE
cmd.feedback("push")
cmd.feedback("disable","executive","actions")
# your basic rainbow...
list = [
(0,0,255),
(0,0,255),
(0,128,255),
(0,255,255),
(0,255,128),
(0,255,0),
(128,255,0),
(255,255,0),
(255,128,0),
(255,0,0),
(255,0,0)
]
if reverse:
list.reverse()
#
last = list.pop(0)
cmd.set_color("_000",[last[0]/255.0,last[1]/255.0,last[2]/255.0])
c = 1
for a in list:
for b in range(1,21):
b0 = b/20.0
b1 = 1.0-b0
cname = "_%03d"%c
r = last[0]*b1+a[0]*b0
g = last[1]*b1+a[1]*b0
b = last[2]*b1+a[2]*b0
cmd.set_color(cname,[r/255.0,g/255.0,b/255.0])
c = c + 1
last = a
cas = cmd.index("((byres ("+selection+")) and name ca and not het)")
l = len(cas)
if not len(cas):
return
c = 0
for a in cas:
col = int((200*c)/l)
cmd.color("_%03d"%col,"((%s) and (byres %s`%d))"%(selection,a[0],a[1]))
c = c + 1
cmd.feedback("pop")
def apply_gradient(selection, start_color='blue', end_color='yellow'):
"""
This function applies a gradient to the selection. It works with either
a string color name which exists in the PyMOL color index, or custom RGB
values.
"""
deltas = []
for r, d in selection:
deltas.append(d)
#Get the dynamic range of the deltas
delta_min = min(deltas)
delta_dynrange = max(deltas) - delta_min
#Create a dictionary of colors from PyMOL
color_dict = {}
for col, num in cmd.get_color_indices():
color_dict[col] = cmd.get_color_tuple(num)
#Get the RGB values of the start color
try:
int(start_color[0])
except ValueError:
start_rgb = color_dict[start_color]
else:
start_rgb = start_color
#Get the RGB values of the end color
try:
int(end_color[0])
except ValueError:
end_rgb = color_dict[end_color]
else:
end_rgb = end_color
#Get the dynamic range for RGB values
rgb_dynrange = []
for i in range(3):
rgb_dynrange.append(end_rgb[i]-start_rgb[i])
print(rgb_dynrange)
#Apply the coloring to each residue in the selection
tick = 0
for r, d in selection:
cmd.select(name='gradient', selection='resi {0}'.format(r))
change = (d - delta_min) / delta_dynrange
res_red = start_rgb[0] + change * rgb_dynrange[0]
res_gre = start_rgb[1] + change * rgb_dynrange[1]
res_blu = start_rgb[2] + change * rgb_dynrange[2]
cmd.set_color('grad{0}'.format(tick), [res_red, res_gre, res_blu])
cmd.color('grad{0}'.format(tick), 'gradient')
tick += 1
def rot_color(vals):
nbins = 10
vals.sort(key=lambda x:x[1])
# print "End sort: "+str(len(vals))+" : "+str(nbins)
# Coloring scheme...
j = 0
rgb = [0.0,0.0,0.0]
sel_str = ""
for i in range(len(vals)):
if int(len(vals)/nbins) == 0 or i % int(len(vals)/nbins) == 0:
hsv = (colorsys.TWO_THIRD - colorsys.TWO_THIRD * float(j) / (nbins-1), 1.0, 1.0)
#convert to rgb and append to color list
rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])
if j < nbins-1:
j += 1
cmd.set_color("RotProbColor"+str(i), rgb)
cmd.color("RotProbColor"+str(i), str(vals[i][0]))
def convert_color_RGB(colorr): ''' RGB colores are not defined in pymol. convert_color_RBG function defines RGB colors Input : '#3300FF' Output : "RGB_blue" ( which we have defined to be [51 , 0 , 255] ) ''' cmd.set_color( 'RGB_blue' , [51 , 0 , 255] ) cmd.set_color( 'RGB_green' , [51 , 153 , 51] ) cmd.set_color( 'RGB_Lblue' , [51 , 153 , 255] ) cmd.set_color( 'RGB_grey' , [128 , 128 , 128] ) cmd.set_color( 'RGB_brown' , [139 , 69 , 19] ) cmd.set_color( 'RGB_purple' , [153 , 30 , 255] ) cmd.set_color( 'RGB_gold' , [205 , 173 , 0] ) cmd.set_color( 'RGB_red' , [255 , 0 , 51] ) cmd.set_color( 'RGB_orange' , [255 , 102 , 0] ) if colorr == "#3300FF": return "RGB_blue" elif colorr == "#339933": return "RGB_green" elif colorr == "#3399FF": return "RGB_Lblue" elif colorr == "#808080": return "RGB_grey" elif colorr == "#8B4513": return "RGB_brown" elif colorr == "#991EFF": return "RGB_purple" elif colorr == "#CDAD00": return "RGB_gold" elif colorr == "#FF0033": return "RGB_red" elif colorr == "#FF6600": return 'RGB_orange' else: return ''
import cmd
import csv
#f = open("coloring.csv", "rb")
#reader = csv.reader(f, delimiter=",")
#cmd.set_color(a, [0.00 , 0.53 , 0.22])
#cmd.set_color dblue= [0.05 , 0.19 , 0.57]
cmd.color( 'gren' , "4QS1 and resi 71-280")
cmd.set_color( 'gren' , [51 , 70 , 255] )
# 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):
# Determine rgb of new color
fx = j/num_steps
color_list = color_gradients[i](fx)
# Create a new color
color_name = "col%s%i" % (u,j)
cmd.set_color(color_name,color_list)
# Apply the color to step j of trajectory u
cmd.color(color_name,t)
def convert_color_RGB(colorr):
'''
RGB colors are not defined in pymol.
convert_color_RBG function defines RGB colors
Input : '#3300FF'
Output : "RGB_blue" ( which we have defined to be [51 , 0 , 255] )
'''
cmd.set_color('RGB_blue', [51, 0, 255])
cmd.set_color('RGB_green', [51, 153, 51])
cmd.set_color('RGB_Lblue', [51, 153, 255])
cmd.set_color('RGB_grey', [128, 128, 128])
cmd.set_color('RGB_brown', [139, 69, 19])
cmd.set_color('RGB_purple', [153, 30, 255])
cmd.set_color('RGB_gold', [205, 173, 0])
cmd.set_color('RGB_red', [255, 0, 51])
cmd.set_color('RGB_orange', [255, 102, 0])
if colorr == "#3300FF":
return "RGB_blue"
elif colorr == "#339933":
return "RGB_green"
elif colorr == "#3399FF":
return "RGB_Lblue"
elif colorr == "#808080":
return "RGB_grey"
elif colorr == "#8B4513":
return "RGB_brown"
elif colorr == "#991EFF":
return "RGB_purple"
elif colorr == "#CDAD00":
return "RGB_gold"
elif colorr == "#FF0033":
return "RGB_red"
elif colorr == "#FF6600":
return 'RGB_orange'
else:
return 'white'
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):
# Determine rgb of new color
fx = j / num_steps
color_list = color_gradients[i](fx)
# Create a new color
color_name = "col%s%i" % (u, j)
cmd.set_color(color_name, color_list)
# Apply the color to step j of trajectory u
cmd.color(color_name, t)
def colors(scheme="",_self=cmd):
pymol=_self._pymol
cmd=_self
if scheme=="jmol":
cmd.set("auto_color",0)
cmd.set_color("hydrogen",[1.000,1.000,1.000])
cmd.set_color("carbon",[0.567,0.567,0.567])
cmd.set_color("nitrogen",[0.189,0.315,0.976])
cmd.set_color("oxygen",[1.000,0.051,0.051])
cmd.set_color("fluorine",[0.567,0.882,0.314])
cmd.set_color("sulfur",[1.000,1.000,0.189])
cmd.color("carbon","elem c")
cmd.recolor()
