[PyMOL] disappearing surface representation

[Karen C. <kch...@uv...>]

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 ***"