# # 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