[Chimera-users] Two transparent models

Tom Goddard goddard at cgl.ucsf.edu
Thu Aug 14 10:03:27 PDT 2008

On Aug 11, 2008, at 12:15 PM, Daniel Wilson wrote:
> Dear Elaine,
> I realise that there have already been requests about fixing the bug 
> in Chimera for displaying two transparent maps at the same time, so I 
> guess I am just asking whether this is likely to be fixed anytime 
> soon? We are desperate to use this function for a figure for a paper :)
> THanks,
> Daniel
> Dr. Daniel N. Wilson
> Gene Center Munich
> Department of Chemistry and Biochemistry
> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
> 81377 Munich, Germany
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.


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