#
# use ChimeraX 1.6 daily build from Jan 5 2023 or newer
#
windowsize 600 800
set bg_color white
# orthographic projection (turn off perspective, in which closer=larger)
camera ortho
# 4lde active-state B2AR with antibody and high-affinity agonist residue P0G;
# PDB file from OPM includes estimated boundaries of membrane hydrophobic core
#  https://opm.phar.umich.edu/proteins/1102
open 4lde-OPM.pdb
define plane :dum@N name inner color moccasin thickness 0.5
define plane :dum@O name outer color moccasin thickness 0.5
trans #1.3-4 80
# inactive B2AR dimer with carazolol (partial inverse agonist) residue CAU
open 2rh1
delete /B
# delete residues not from ADRB2_HUMAN as reported in Log
del #1 & protein & ~:1029-1348
del #2 & protein & ~:1-230,263-365
hide atoms
mm #2 to #1
preset licorice
view
rainbow
color modify saturation - 50
define axis perhelix true rad 0.75
# hide axes for some of the non-transmembrane helices
hide #1.5.5,8,11 #2.2.5
color #1 & C plum targ ra
color #2 & C gray targ ra
light gentle
# show agonist, define centroids of ring systems
show :p0g
define centroid :p0g@cag,cah,cai,caj,cat,cav rad 0.8 col magenta
define centroid :p0g@cak,cal,cam,cas,oar,naq,cau,caw,cax,cay rad 0.8 col magenta