RE: [PyMOL] disappearing surface representation

[Warren D. <wa...@de...>]

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

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> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Karen Champagne
> Sent: Tuesday, May 10, 2005 1:48 PM
> To: pym...@li...
> 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 ***"
> 
> 
> 
> 
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