Sample POV-Ray Rendering First convert dioxin.mol2 to the dioxin.inc file: babel -imol2 dioxin.mol2 -opov dioxin.inc Then type (POV-Ray 3.1) povray +V +A +D0 +Q9 +W320 +H200 +I dioxin.pov (POV-Ray 3.5) povray +V +A +D0 +Q9 +W320 +H200 dioxin.pov for a demo.