fomightez · March 11, 2026 15:58
diff --git a/render_as_cartoon_only_MaxPerformance.ipy b/render_as_cartoon_only_MaxPerformance.ipy
 # Compromises quality for speed/efficiency
 # REPLACE CONTENT OF THE CELL WITH THIS CODE, or use a varation of it if you just prefer cartoon represenation for your use:
 text_2_save_templ = '''#!/usr/bin/python

 import sys, os

 # pymol environment
 moddir='/opt/pymol-svn/modules'
 sys.path.insert(0, moddir)
 os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')

 import pymol
 cmd = pymol.cmd
 # end of set-up



 # get the structure & load it into PyMol
 cmd.fetch('the_STRUCTURE_PLACEHOLDER')
 cmd.zoom()

 # set my preferred starting point for representation
 cmd.set ("ray_opaque_background", 0)
 cmd.set ("cartoon_fancy_helices", 1)
 cmd.bg_color ("white")
 cmd.set ("cartoon_side_chain_helper", "on")
 #cmd.hide ("everything", "all")

 #set desired orientation
 def set_my_view():
    cmd.set_view("the_ORIENTATION_PLACEHOLDER")
 set_my_view()

 # Generate an image for a few color combinations ( NOT ALL)
 number_shuffles_to_run = the_SHUFFLE_NUMBER_PLACEHOLDER

 # define any custom colors
 def hex_to_rgb(value):
    #based on https://stackoverflow.com/a/214657/8508004
    value = value.lstrip('#')
    lv = len(value)
    return tuple(int(value[i:i + lv // 3], 16) for i in range(0, lv, lv // 3))
 cmd.set_color ("my_color", [*hex_to_rgb("#7D80B0")])

 # specify the palette of colors to use
 color_list = the_COLOR_LIST_PLACEHOLDER

 # determine ids of loaded chains, see `iterating over residue secondary structure and color.md`
 names_of_structures_loaded = cmd.get_names()
 the_chains = cmd.get_chains(names_of_structures_loaded[0])
 print ("There are {} chains.".format(len(the_chains)))
 stored.elems = []
 cmd.iterate ("metals", "stored.elems.append(elem)")
 the_metals = list(set(stored.elems))
 if the_metals:
    print ("There are {} metal ions.".format(len(the_metals)))
 the_chains_n_metals = the_chains + the_metals

 the_chains_as_selections = ["chain {}".format(x) for x in the_chains]
 the_metals_as_selections = ["resn {}".format(x) for x in the_metals]
 items_to_color = the_chains_as_selections + the_metals_as_selections

 #base display styling
 #cmd.show ("surface", "polymer.protein")
 #show metals as speheres
 for sm in the_metals_as_selections:
    cmd.show ("spheres", sm)
 cmd.set ("fog_start", 0.70) #move fog back farther so not hitting main part as much

 import random
 from itertools import cycle
 f=open('color_lists.txt','w') 
 cmd.util.performance(100)
 for x in range(number_shuffles_to_run):
    random.seed(x)
    random.shuffle(color_list)
    pymol_colors = cycle(color_list)
    applied = []
    for i in items_to_color:
        clr_4_now = next(pymol_colors)
        cmd.color(clr_4_now, i)  # Colors spheres and other representations
        cmd.set("cartoon_color", clr_4_now, i)  # Colors cartoons specifically
        applied.append((i,clr_4_now))
    cmd.png("img_{}.png".format(x), width=500, height=500, dpi=72, ray=1, quiet=0)
    f.write("seed {}: {}\\n".format(x,applied)) #note double 
    # backslash to escape necessary or get `SyntaxError: EOL while scanning string 
    # literal` when hit that line
    f.flush();os.fsync(f.fileno()) #added so even if task gets killed, I get 
    # color list for what processed thus far; based on 
    #https://stackoverflow.com/a/19756479/8508004
 f.close()
 '''
 text_2_save = text_2_save_templ.replace("the_STRUCTURE_PLACEHOLDER",PDB_id_code)
 text_2_save = text_2_save.replace("the_COLOR_LIST_PLACEHOLDER",str(my_colors_as_strings))
 text_2_save = text_2_save.replace("the_ORIENTATION_PLACEHOLDER",orientation_string)
 text_2_save = text_2_save.replace("the_SHUFFLE_NUMBER_PLACEHOLDER",str(shuffles_to_do))
 %store text_2_save >script.py
 !pymol -cq script.py
	# Compromises quality for speed/efficiency
	# REPLACE CONTENT OF THE CELL WITH THIS CODE, or use a varation of it if you just prefer cartoon represenation for your use:
	text_2_save_templ = '''#!/usr/bin/python

	import sys, os

	# pymol environment
	moddir='/opt/pymol-svn/modules'
	sys.path.insert(0, moddir)
	os.environ['PYMOL_PATH'] = os.path.join(moddir, 'pymol/pymol_path')

	import pymol
	cmd = pymol.cmd
	# end of set-up



	# get the structure & load it into PyMol
	cmd.fetch('the_STRUCTURE_PLACEHOLDER')
	cmd.zoom()

	# set my preferred starting point for representation
	cmd.set ("ray_opaque_background", 0)
	cmd.set ("cartoon_fancy_helices", 1)
	cmd.bg_color ("white")
	cmd.set ("cartoon_side_chain_helper", "on")
	#cmd.hide ("everything", "all")

	#set desired orientation
	def set_my_view():
	cmd.set_view("the_ORIENTATION_PLACEHOLDER")
	set_my_view()

	# Generate an image for a few color combinations ( NOT ALL)
	number_shuffles_to_run = the_SHUFFLE_NUMBER_PLACEHOLDER

	# define any custom colors
	def hex_to_rgb(value):
	#based on https://stackoverflow.com/a/214657/8508004
	value = value.lstrip('#')
	lv = len(value)
	return tuple(int(value[i:i + lv // 3], 16) for i in range(0, lv, lv // 3))
	cmd.set_color ("my_color", [*hex_to_rgb("#7D80B0")])

	# specify the palette of colors to use
	color_list = the_COLOR_LIST_PLACEHOLDER

	# determine ids of loaded chains, see `iterating over residue secondary structure and color.md`
	names_of_structures_loaded = cmd.get_names()
	the_chains = cmd.get_chains(names_of_structures_loaded[0])
	print ("There are {} chains.".format(len(the_chains)))
	stored.elems = []
	cmd.iterate ("metals", "stored.elems.append(elem)")
	the_metals = list(set(stored.elems))
	if the_metals:
	print ("There are {} metal ions.".format(len(the_metals)))
	the_chains_n_metals = the_chains + the_metals

	the_chains_as_selections = ["chain {}".format(x) for x in the_chains]
	the_metals_as_selections = ["resn {}".format(x) for x in the_metals]
	items_to_color = the_chains_as_selections + the_metals_as_selections

	#base display styling
	#cmd.show ("surface", "polymer.protein")
	#show metals as speheres
	for sm in the_metals_as_selections:
	cmd.show ("spheres", sm)
	cmd.set ("fog_start", 0.70) #move fog back farther so not hitting main part as much

	import random
	from itertools import cycle
	f=open('color_lists.txt','w')
	cmd.util.performance(100)
	for x in range(number_shuffles_to_run):
	random.seed(x)
	random.shuffle(color_list)
	pymol_colors = cycle(color_list)
	applied = []
	for i in items_to_color:
	clr_4_now = next(pymol_colors)
	cmd.color(clr_4_now, i) # Colors spheres and other representations
	cmd.set("cartoon_color", clr_4_now, i) # Colors cartoons specifically
	applied.append((i,clr_4_now))
	cmd.png("img_{}.png".format(x), width=500, height=500, dpi=72, ray=1, quiet=0)
	f.write("seed {}: {}\\n".format(x,applied)) #note double
	# backslash to escape necessary or get `SyntaxError: EOL while scanning string
	# literal` when hit that line
	f.flush();os.fsync(f.fileno()) #added so even if task gets killed, I get
	# color list for what processed thus far; based on
	#https://stackoverflow.com/a/19756479/8508004
	f.close()
	'''
	text_2_save = text_2_save_templ.replace("the_STRUCTURE_PLACEHOLDER",PDB_id_code)
	text_2_save = text_2_save.replace("the_COLOR_LIST_PLACEHOLDER",str(my_colors_as_strings))
	text_2_save = text_2_save.replace("the_ORIENTATION_PLACEHOLDER",orientation_string)
	text_2_save = text_2_save.replace("the_SHUFFLE_NUMBER_PLACEHOLDER",str(shuffles_to_do))
	%store text_2_save >script.py
	!pymol -cq script.py
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