[Chimera-users] Memory allocation

Thomas Goddard goddard at cgl.ucsf.edu
Tue Sep 12 18:22:09 PDT 2006

Hi Brittany,

  Thanks for the detailed information.  I do not think memory is the
problem.  Display of 58,000 atoms (pdb 1uf2) in ball and stick took
10 seconds on my 4 year old laptop.  That is the time to make the
intial drawing.  Then it update at about 2 frames per second when
rotating the model on this rather old machine.

  Your problem is likely caused by one of two issues.  First, if your
"molecule-type objects" contain many (tens or hundreds) small rings
within a residue then Chimera will bog down trying to compute the
chemical atom types (aromaticity...).  This is a problem we have
recently analyzed when using Chimera with molecules that do not have
reasonable chemical structure.  We plan on fixing this problem by
being able to tag molecules in Chimera as "non-chemical".  But we do
not have a version of Chimera available with that feature yet.  So
currently the only solution is to modify your non-molecule model using
multiple residues to avoid having many rings in a single residue.  The
ring computation is not done in wire display style but is invoked when
switching to ball and stick style because atom radii are needed and
are based on the chemical types.

  The second possible problem is that you are not using hardware
accelerated 3D graphics.  On Linux systems you usually need to install
a graphics driver to get hardware acceleration.  Windows and Mac
systems usually already have the appropriate driver.  Rendering
computations can be 100 times slower if it is done in software instead
of by the graphics chip.  Ball and stick display style is much more
time consuming to render than wire frame.  If you are able to rotate
the 64,000 atom ball and stick model after it is first displayed (15
minutes) and it updates reasonably fast (> 1 frame per second) then
you have hardware acceleration and this is not the problem.


> From: "Brittany Morgan" <brmorgan at clarku.edu>
> To: "'Thomas Goddard'" <goddard at cgl.ucsf.edu>
> Subject: RE: [Chimera-users] Memory allocation
> Date: Tue, 12 Sep 2006 20:52:39 -0400
>   I am working with molecules, and it has problems redrawing them in
> ball-and-stick representation, although I expect that at larger system sizes
> other functions will start slowing down as well. If I look at the memory
> usage while it is redrawing them, Chimera seems to be using only about 1/4
> of the available memory, but creating a paging file nonetheless. It will
> work, it just takes about 15 minutes to redraw about 64,000 atoms, and I
> need to go to system sizes much larger. If I need more memory, that is
> possible, I just wasn't sure if that was the issue because it didn't appear
> that Chimera was using all of the available memory. I am using Chimera in a
> non-standard way (I'm not displaying proteins, but rather many small
> (unrealistic) molecule-type objects).
> Thank you for your help!
> Brittany

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