Karen, Your problem is that opaque_background is turned off, so trasparency is being handled via alpha-channel, and not via blending. If you re-enable this setting (remove "set ray_opaque_background, off") then I think you'll get the kind of effect you seek.
Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Karen Champagne > Sent: Tuesday, May 10, 2005 1:48 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] disappearing surface representation > > Hi Everyone, > > I am trying to make a movie using Pymol that shows the > surface of my protein disappear as it rotates. For example I > rotate it around the y-axis for 360 degrees in 2 degree > increments. And have it become more transparent over 90 > degrees until it disappears altogether and just the cartoon > is showing underneath. I use these commands: > > mvSet 1-90,transparency,0.0,1.0 > mvSinrot 1-180,y,360 > > So I generate the 180 .png images just fine. The problem > arises when I try to import the sequence of frames into > quicktime. I have Quicktime Pro version 7.0. What happens > is that quicktime still sees the surface, even though when I > open this same file in preview the surface is clearly not > there. This makes it so that the cartoon underneath is never > really discernible in the movie. I'm not sure why quicktime > would be reading the file differently? Or if there is > anything I can do about it. Has anyone seen this before, and > found a way around? > > I pasted my script below for you to have a look at. > > Thanks, > Karen > > > > # Example script for movie.py for PyMOL > # > run movie.pml > > # initialize everything to look nice > #initalize > load oct_PRPP_model.pdb > > orient (orient) > full > frame 1 > mset 1 x3000 > > # clear the movie.py memory > mvClear > > set cartoon_fancy_helices = 1 > set cartoon_flat_sheets = 1 > #set cartoon_smooth_loops = 0 > bg_color white > set ray_trace_fog = 0 > set ray_opaque_background, off > > hide everything, > show cartoon > > color slate, chain A > color slate, chain B > color slate, chain C > color slate, chain D > > color lime, chain E > color lime, chain F > color lime, chain G > color lime, chain H > > select PRPP, resid 4007 > color red, PRPP > show spheres, PRPP > show lines, PRPP > set sphere_scale = 0.4 > > show spheres, chain I > show lines, chain I > select PO4, chain I > color orange, chain I > > set transparency, 1.0 > show surface > > set_view (\ > 0.093076237, 0.165435120, -0.981818616,\ > 0.187504619, 0.965541244, 0.180467844,\ > 0.977843046, -0.200893298, 0.058849588,\ > -0.000079998, -0.000131577, -354.491577148,\ > 117.667976379, 42.596172333, -10.524626732,\ > 277.953521729, 431.030609131, 0.000000000 ) > > #store orientation matrix to recall at end of movie mmatrix store > > # fade in and fade out > mvSet 1-90,transparency,0.0,1.0 > mvSinrot 1-180,y,360 > movie > viewport 1024,768 > # turn ray tracing on: > set ray_trace_frame = 1 > # turn background pixels transparent > set ray_opaque_background, off > # turn antialias on: > set antialias = 1 > # turn off caching: > set cache_frames = 0 > # output rendered movie frames in PNG format: > mpng 360y, 1 > #movie > # tell me when you're done! > system echo " *** FINISHED ***" > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by Oracle Space Sweepstakes > Want to be the first software developer in space? > Enter now for the Oracle Space Sweepstakes! > http://ads.osdn.com/?ad_id=7393&alloc_id=16281&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
