Ticket #1267: ecoli_ribosome.cxc

#
# ChimeraX command script to setup E coli ribosome antibiotic virtual reality scene.
# Tested with HTC Vive and Geforce GTX 1080 graphics.
#
open 4v7s

# Simple lighting so renders fast enough so VR does not stutter
light simple

# Delete second copy of ribosome
del /ca-dz

# Delete hydrogen bonds.
close #1.1

# Show RNA nucleotides as cylinders
#rungs #1
hide nucleic atoms
show nucleic ribbons

# For residues near antibiotic telithromycin
# show full side chains instead of rungs near ligand
select zone :tel 10 residues true
#rungs hide sel
show sel atoms
style sel stick
color sel byhet
select clear

# Show drug in ball and stick
style :tel ball

# Color antibiotic purple
color :tel&C purple

# Color numerous magnesium ions.
color @MG byelement

# Color antibiotic resistance methylation residue A2503 yellow
# and C2 and C8 methylation sites orange.
color /BA:2503&C yellow
color /BA:2503@C2,C8 orange atoms

# Add xray density near drug
open 4v7s from eds
volume #2 region 108,68,123,151,100,153 level 0.2
wait 1
surface zone #2 near :tel distance 10

# Show transparent volume surface.  Mesh lines shimmer too much.
vol #2 transparency .8 style surface

# Show initial view in VR.
vr on roomPosition -4.85,-1.2722,1.1477,-64.092,-1.6333,4.4738,-1.9431,-59.467,-0.51761,-2.1966,-4.6222,13.089