[Chimera-users] multiple transparent models

Tom Goddard goddard at cgl.ucsf.edu
Thu Feb 14 11:06:29 PST 2008

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.


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