[Chimera-users] multiple transparent models

William Jeffrey Triffo triffo at rice.edu
Thu Feb 14 11:10:43 PST 2008


in my case it appeared that the order changed between two sessions. I 
switched a file name (told chimera to load a binned file by default, 
rather than loading the full file + the 2x subsampled (binned) version), 
but the order in the chimera .py session file remained the same.

I was able to generate a close enough 'look' to what I was after by 
clicking 'surface' and then 'solid' again. I do not know why that helped 
out, but it restored the model to its previous order in the rendering.


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

Jeff Triffo
Auer Group, Donner Lab, Lawrence Berkeley National Laboratory
Raphael Group, Bioengineering Department, Rice University
Medical Scientist Training Program (MSTP), Baylor College of Medicine
phone (Berkeley): 510-486-7940
fax   (Berkeley): 510-486-6488   

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