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. Tom

From: "Brittany Morgan" <brmorgan@clarku.edu> To: "'Thomas Goddard'" <goddard@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