[Chimera-users] Transparency doesn't look right

Tom Goddard goddard at cgl.ucsf.edu
Tue Jul 20 17:55:37 PDT 2010

Hi Mitalee

   This is a Chimera limitation.  Two or transparent models will not be 
shown correctly.  Transparency works correctly only when at most one 
model is transparent.  You have the volume data displayed in "solid" 
style which is a kind of transparent rendering, and you have a surface 
model which is transparent.  How defective the transparency looks 
depends on the order the models were opened in Chimera (or maybe it 
depends on which has higher model id number, don't recall).  In any 
case, both orders look seriously wrong.  If you reverse the order of 
opening your two models I think your surface will remain totally 
invisible until it becomes 0% transparent when it will suddenly appear.

   This limitation is a rather fundamental design problem in Chimera.  
Chimera draws the models one at a time.  A model that is drawn after 
another model can only appear in front of the first model.  Chimera 
first draws all opaque models, then draws all transparent models.

   If you look at the termite gut video I made


where surfaces fade in you'll see at the start of the fade in, a black 
blob suddenly appears representing the object.  This is the same bad 
behavior you see in your case, but your surface is white (the background 
color) and is in front of the volume data making it look especially bad.

   This problem has arisen many times in, especially in movie making 
where transparency is used to fade objects in and out.  I have an idea 
for a solution although it is not yet implemented.  But we just hired 
Daren Weber to work on animation improvements in Chimera and perhaps he 
can try this.  The idea is to enhance the movie command to add a 
"crossfade" option.  You would display the volume, then use a command 
like "movie crossfade 25" then show the opaque surface.  The command 
would take the image right before the command was issued and the next 
image and linearly blend them over 25 frames.  This would be useful for 
many fade scenarios.  It is limited in that it won't be able to have 
models moving and a fade occurring at the same time since that is not 
simply a linearly blending of two images.

   I'll see if Darren is interested in trying to add this if you are 

   If you do not want to wait for this, another option is to record your 
movie without the fade -- just have the surface suddenly appear.  Then 
drop the movie into an video editing program like Final Cut and add the 
crossfade with that software.

> Hi Tom,
> I was using the surft command, trying to make a segment appear inside of a
> cmap file. Basically, I have a cmap file open and visible, and I want to
> show the segmented cell appear slowly. My problem is that when I set the
> transparency of the segmented cell to 100 (i.e. surft 100 #0), it doesn't
> exactly become transparent, or what I thought would be transparent. When I
> enter this command, it makes the entire image transparent at that point
> (so the shape of the segmented cell is preserved and matches the
> background. I've attached an image of what I got as a result. Is there a
> way to make preserve the cmap image and just make the segmented cell
> overlay onto it without completely "removing" the section where the
> segmented cell will appear?
> Thanks,
> Mitalee

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