By default, PyMOL only shows the front-most transparent surface. set transparency_mode, 1 and ray to reliably combine all transparent surfaces in all displayed objects. DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD
_____ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Andreas Forster Sent: Tuesday, April 10, 2007 4:12 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] transparency cross-fading Hey all, I've run into the following problem while making some movies with MacPyMOL 0.99rc6. I have a protein in surface representation that I start with transparency = 0 and a cavity (voidoo-created map) as surface with transparency = 1. In other words, the protein surface is visible, the cavity is not. When I cross-fade the transparencies, like so: for i in range (1, 41): cmd.set ("transparency", i*0.025, "protein") cmd.set ("transparency", 1-(0.016*i), "cavity") cmd.ray cmd.png ("fadeOut_%02d" %i) the protein disappears and the cavity appears gracefully. However, those parts of the cavity hidden behind a wall of protein don't fade in as the protein surface disappears. They only appear when the protein surface transparency has reached 1, and there is a sudden jerk between the second-to-last and the last image created by above script as the cavity becomes fully visible. I remember that this issue has come up before but don't remember if there is a solution. Could someone enlighten me please? Thanks. Andreas
