[Chimera-users] Two transparent models

Tom Goddard goddard at cgl.ucsf.edu
Thu Aug 14 10:16:54 PDT 2008

Daniel Wilson wrote:
> Hi Tom,
> For what we want, the combination of one transparent model with one mesh is working. However, I will play around with the raytracing a few examples with povray and see if it looks better. Seems to make more sense before you invest time in a script.
> The other thing I noticed is that you lose transparency on a whole volume when you color zone one region of it? or am I making something wrong? Is it not possible to have a single volume with two different colours and transparent?
> Thanks for you advice and kind offer,
> regards
> Daniel
> Tom Goddard <goddard at cgl.ucsf.edu> schrieb :
>> Hi Daniel,
>>   The incorrect transparency in Chimera when 2 or more models are 
>> transparent is very difficult to fix and will not be fixed any time 
>> soon.  The trouble is that Chimera draws each model separately and it is 
>> not possible to correctly handle transparency without intermixing the 
>> drawing of parts of models (in depth order).
>>   If you use Chimera image saving in the POVray raytracing mode it will 
>> correctly show multiple transparent models.  The trouble is that this 
>> takes a long time to render and adjusting the levels of transparency 
>> many times to get the right appearance may be tedious.
>>   It would be possible to make a script that combines the currently 
>> displayed map surfaces into a single model and hides all the original 
>> models so that multimodel transparency would appear correct on-screen.  
>> But the combined model would not update when you changed the 
>> transparency, color, ... settings of the separate maps.  It would 
>> require rerunning the script that makes the single model.  This would be 
>> tedious to use.  But if you think it worth trying I can write the script 
>> and send it to you.  It would not work for transparent molecular models 
>> (ribbons and atoms), just surfaces.
>>     Tom

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