so, 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. -Jeff 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