pymol-users

[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 ***"

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

. 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:wa...@de...      
 

> -----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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