# Copyright 2019 Simon & Garfunkel
import colorsys,sys
from pymol import cmd
import numpy as np

def rithm():
    cmd.bg_color("white")
#    cmd.load("view*")
    cmd.set('defer_builds_mode', 3)
    cmd.set("antialias", 5)
    cmd.set("ray_trace_mode", 6)
    cmd.hide()
    cmd.select("mito_lipids", "resname POPC or resname SLPE or resname PLPC")
    cmd.select("tlx", "resname TLX*")
    cmd.color("hotpink", "resname 3PP")
    cmd.color("ruby", "resname BDL")
    cmd.color("marine", "resname BTL")
    cmd.show_as("sticks", "mito_lipids or tlx")
    cmd.select("lipids_H", "hydro and (resname POPC or resname SLPE or resname PLPC or resname TLX*)")
    cmd.hide("everything", "lipids_H")
    cmd.select("bodipy", "resname BDL or resname 3PP or resname BTL")
    cmd.show_as("sticks", "bodipy")
    cmd.set("stick_radius", 0.6, "bodipy")
#  cmd.show("spheres", "bodipy")
#  cmd.set("sphere_transparency",0.2)
#    cmd.set("stick_color", "white", "bodipy")
    cmd.select("perox_o", "name OP* and tlx")
    cmd.select("oxy", "name O* and (mito_lipids or tlx)")
    cmd.select("phos", "name P* and (mito_lipids or tlx)")
    cmd.select("carbon_MITO", "name *C* and mito_lipids")
    cmd.select("carbon_TLX", "name *C* and tlx")
    cmd.color("gray80", "carbon_MITO")   
    cmd.color("tv_green", "carbon_TLX")  
    cmd.select("water", "resname SOL") 
    cmd.select("na", "resname NA") 
    cmd.select("cl", "resname CL") 
    cmd.color("salmon", "cl") 
    cmd.color("yellow", "na") 
    cmd.show_as("spheres", "na or cl")
    cmd.set("sphere_scale", 0.5, "na or cl")
    cmd.show_as("surface", "water")
    cmd.set("transparency", 0.5)
    cmd.color("aquamarine", "water")
    cmd.set("ray_shadows", "off")
    cmd.set("surface_solvent", "on")
    cmd.set("transparency_mode", 1)

#    run drawBoundingBox.py
#drawBoundingBox padding=-13.0, linewidth=2.0, r=0, g=0, b=0    

22aefc72f4243a83e51161736ca08ef5b331ae7b
<mask token>

<mask token>


def rithm():
    cmd.bg_color('white')
    cmd.set('defer_builds_mode', 3)
    cmd.set('antialias', 5)
    cmd.set('ray_trace_mode', 6)
    cmd.hide()
    cmd.select('mito_lipids', 'resname POPC or resname SLPE or resname PLPC')
    cmd.select('tlx', 'resname TLX*')
    cmd.color('hotpink', 'resname 3PP')
    cmd.color('ruby', 'resname BDL')
    cmd.color('marine', 'resname BTL')
    cmd.show_as('sticks', 'mito_lipids or tlx')
    cmd.select('lipids_H',
        'hydro and (resname POPC or resname SLPE or resname PLPC or resname TLX*)'
        )
    cmd.hide('everything', 'lipids_H')
    cmd.select('bodipy', 'resname BDL or resname 3PP or resname BTL')
    cmd.show_as('sticks', 'bodipy')
    cmd.set('stick_radius', 0.6, 'bodipy')
    cmd.select('perox_o', 'name OP* and tlx')
    cmd.select('oxy', 'name O* and (mito_lipids or tlx)')
    cmd.select('phos', 'name P* and (mito_lipids or tlx)')
    cmd.select('carbon_MITO', 'name *C* and mito_lipids')
    cmd.select('carbon_TLX', 'name *C* and tlx')
    cmd.color('gray80', 'carbon_MITO')
    cmd.color('tv_green', 'carbon_TLX')
    cmd.select('water', 'resname SOL')
    cmd.select('na', 'resname NA')
    cmd.select('cl', 'resname CL')
    cmd.color('salmon', 'cl')
    cmd.color('yellow', 'na')
    cmd.show_as('spheres', 'na or cl')
    cmd.set('sphere_scale', 0.5, 'na or cl')
    cmd.show_as('surface', 'water')
    cmd.set('transparency', 0.5)
    cmd.color('aquamarine', 'water')
    cmd.set('ray_shadows', 'off')
    cmd.set('surface_solvent', 'on')
    cmd.set('transparency_mode', 1)

import colorsys, sys
from pymol import cmd
import numpy as np


def rithm():
    cmd.bg_color('white')
    cmd.set('defer_builds_mode', 3)
    cmd.set('antialias', 5)
    cmd.set('ray_trace_mode', 6)
    cmd.hide()
    cmd.select('mito_lipids', 'resname POPC or resname SLPE or resname PLPC')
    cmd.select('tlx', 'resname TLX*')
    cmd.color('hotpink', 'resname 3PP')
    cmd.color('ruby', 'resname BDL')
    cmd.color('marine', 'resname BTL')
    cmd.show_as('sticks', 'mito_lipids or tlx')
    cmd.select('lipids_H',
        'hydro and (resname POPC or resname SLPE or resname PLPC or resname TLX*)'
        )
    cmd.hide('everything', 'lipids_H')
    cmd.select('bodipy', 'resname BDL or resname 3PP or resname BTL')
    cmd.show_as('sticks', 'bodipy')
    cmd.set('stick_radius', 0.6, 'bodipy')
    cmd.select('perox_o', 'name OP* and tlx')
    cmd.select('oxy', 'name O* and (mito_lipids or tlx)')
    cmd.select('phos', 'name P* and (mito_lipids or tlx)')
    cmd.select('carbon_MITO', 'name *C* and mito_lipids')
    cmd.select('carbon_TLX', 'name *C* and tlx')
    cmd.color('gray80', 'carbon_MITO')
    cmd.color('tv_green', 'carbon_TLX')
    cmd.select('water', 'resname SOL')
    cmd.select('na', 'resname NA')
    cmd.select('cl', 'resname CL')
    cmd.color('salmon', 'cl')
    cmd.color('yellow', 'na')
    cmd.show_as('spheres', 'na or cl')
    cmd.set('sphere_scale', 0.5, 'na or cl')
    cmd.show_as('surface', 'water')
    cmd.set('transparency', 0.5)
    cmd.color('aquamarine', 'water')
    cmd.set('ray_shadows', 'off')
    cmd.set('surface_solvent', 'on')
    cmd.set('transparency_mode', 1)

# Copyright 2019 Simon & Garfunkel
import colorsys,sys
from pymol import cmd
import numpy as np

def rithm():
    cmd.bg_color("white")
#    cmd.load("view*")
    cmd.set('defer_builds_mode', 3)
    cmd.set("antialias", 5)
    cmd.set("ray_trace_mode", 6)
    cmd.hide()
    cmd.select("mito_lipids", "resname POPC or resname SLPE or resname PLPC")
    cmd.select("tlx", "resname TLX*")
    cmd.color("hotpink", "resname 3PP")
    cmd.color("ruby", "resname BDL")
    cmd.color("marine", "resname BTL")
    cmd.show_as("sticks", "mito_lipids or tlx")
    cmd.select("lipids_H", "hydro and (resname POPC or resname SLPE or resname PLPC or resname TLX*)")
    cmd.hide("everything", "lipids_H")
    cmd.select("bodipy", "resname BDL or resname 3PP or resname BTL")
    cmd.show_as("sticks", "bodipy")
    cmd.set("stick_radius", 0.6, "bodipy")
#  cmd.show("spheres", "bodipy")
#  cmd.set("sphere_transparency",0.2)
#    cmd.set("stick_color", "white", "bodipy")
    cmd.select("perox_o", "name OP* and tlx")
    cmd.select("oxy", "name O* and (mito_lipids or tlx)")
    cmd.select("phos", "name P* and (mito_lipids or tlx)")
    cmd.select("carbon_MITO", "name *C* and mito_lipids")
    cmd.select("carbon_TLX", "name *C* and tlx")
    cmd.color("gray80", "carbon_MITO")   
    cmd.color("tv_green", "carbon_TLX")  
    cmd.select("water", "resname SOL") 
    cmd.select("na", "resname NA") 
    cmd.select("cl", "resname CL") 
    cmd.color("salmon", "cl") 
    cmd.color("yellow", "na") 
    cmd.show_as("spheres", "na or cl")
    cmd.set("sphere_scale", 0.5, "na or cl")
    cmd.show_as("surface", "water")
    cmd.set("transparency", 0.5)
    cmd.color("aquamarine", "water")
    cmd.set("ray_shadows", "off")
    cmd.set("surface_solvent", "on")
    cmd.set("transparency_mode", 1)

#    run drawBoundingBox.py
#drawBoundingBox padding=-13.0, linewidth=2.0, r=0, g=0, b=0    
