[Chimera-users] multiple transparent models

Tom Goddard goddard at cgl.ucsf.edu
Tue Feb 19 17:17:50 PST 2008

Correction about multiple transparent models.  By opening models in a 
specific order you can control just how wrong the multi-model 
transparency looks.

Chimera does not correctly display multiple transparent models.  The 
ones drawn last appear in front even if they are behind other 
transparent models.  The order of drawing is the order in which the 
models are opened.  Previously I mistakenly said the drawing order was 
undefined (was looking at x3d scene export code by mistake).  A volume 
solid model is opened when the volume display style is switched to solid 
and is closed when the volume rendering style is switched to surface or 


Tom Goddard wrote:
> Hi Jeff,
>   Chimera does not correctly display transparency when more than one 
> model is shown as transparent.  The transparent models (volumes, 
> molecules, surfaces, ...) are rendered in some order and the last one 
> will always appear in front even if it is physically behind the others 
> -- in other words, the last transparent model paints over the previous 
> transparent models.  (Volumes in solid mode are transparent.)  The 
> trouble is that the order of the models is not predictable.  It seems to 
> be the order in which the models are opened (last one on top), but 
> looking at the C++ code I see that a C++ "map" data structure is being 
> used which does not maintain a predictable order.  You should get the 
> same order each time you open the same set of models in a given order, 
> but what that order will be depends on some C++ internals.  When I have 
> tested with  a small number of models it does appear to be the order in 
> which the models were opened.
>   It would be nice to have a predictable behavior, so I'll see if we can 
> sort them by model id number when rendering.
>     Tom
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