[Chimera-users] Two transparent models and memory leaks

Thomas Goddard goddard at cgl.ucsf.edu
Thu Mar 22 15:57:00 PDT 2007

Hi Christopher,

   Chimera does not correctly handle more than one transparent model. If 
you have two transparent models the one with the higher model id number 
is rendered second and always appears in front of the one with lower 
model id number.  The reason you observed different behaviour (sometimes 
looks ok, sometimes wrong) is because it depends on the model id 
numbers.  If the transparent model in front has the higher id number 
then it looks ok, otherwise it looks wrong.  Opaque models use the 
OpenGL depth buffer and do not have this problem.

   We will need to look into the memory leak (memory is not released 
when closing a session).  What version of Chimera, 1.2352?

   The crash on Windows is very likely caused by running out of memory 
when rendering the image.  Capturing a full screen image with 
supersampling (made 3x larger in both dimensions = 9x more pixels) can 
take significant memory (10 - 100 Mbytes).  A machine with 1 Gbyte of 
memory is barely adequate for displaying ribosome structures (~100,000 
atoms) and large density maps using Chimera.  My Mac machines have 1.5 
Gbytes and 2 Gbytes and I seldom work with atomic models as large as 
yours.  Many EM Chimera users I work with use machines with at least 3 
Gbytes of memory.

   I'll submit a Chimera bug report suggesting we look for the large 
memory allocations done during image saving and try to change the code 
to catch those allocation failures and avoid crashing.

   I don't have a clear picture of the occluded icons problem you 
observe with Chimera displaying full screen on your new Linux machine. 
Could you send a snapshot of that?


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