[Chimera-users] Virus Capsid Reconstruction--Slow Performance

[Carlos Lopez]

Hello,

I am currently trying to make a pseudo-atomic resolution model of a 
virus capsid, but I've run into memory problems whenever I try to 
combine all the asymmetric units together into one large PDB file 
composed of 60 copies of the asymmetric unit arranged using icosahedral 
symmetry. My problem is that I keep running out of memory, and I was 
wondering whether this is normal for the dataset I'm working on. The 
method I use has worked fine for smaller models, so I'm sure I'm running 
into the memory problems because this model is particularly large, but I 
still wanted to check with you guys to see what else I could try.

I first start out with an asymmetric unit composed of 52 copies of 
protein gp24 (PDB ID: 1YUE [monomer] and 1Z1U [hexamer]). That is, I use 
8 hexamers and 4 monomers. The individual chains in the unit are 
stripped to their alpha-carbon backbone by removing all their residues 
(including the solvent) to minimize how much memory they take up. The 
monomer weights 47.274 kDa (with residues), so that gives about 22,347 
total residues for the asymmetric unit. After stripping off everything 
except the backbone, I ended up with a 6.4 MB PDB file. After 
positioning the model, I then run the command sym #1 group i,222r. This 
creates the 59 other copies in the expected locations.

The problem arises when I try to combine all the units together into one 
model. Having all the models open takes up about 10 GB (out of my 
machines 16 GB) worth of memory, though there is still some inactive and 
free memory left. When I then use the copy/combine command, the memory 
required rises steadily until it starts to page out to the swap space 
and bring the machine to a grinding halt. I tried leaving it to run 
overnight (+18 hours), but even then it still wasn't finished.

To recap: I'm trying to do a memory intensive reconstruction. I've already:

1) closed all the other models I'm not working on
2) closed all other programs on the machine
3) removed all the side chains so I'm only working with the alpha-carbon 
backbone
4) tried the chimera --nogui option to send the commands without having 
to render the graphics

It's still having issues, so I was wondering if you had any additional 
ways I can cut down on the memory usage enough to combine the units into 
one map. Here are some of the things I'm still thinking of checking on:

1) Running the job on a computer with no graphics card but more RAM than 
my desktop station. I am able to SSH to the machine and send 
instructions through the console and the chimera --nogui option. Is it a 
problem that it doesn't have a graphics card?

2) Checking for a memory leak in Chimera--I've noticed that sometimes 
not all the memory is given back when I manually close models in the 
model panel. How can I check for sure/fix it from within a session? I've 
been able to deal with this by closing my session and opening it again, 
but it'd be best to be able to do it from within a session.

3) My system keeps saying I still have 4 GB of inactive RAM, though it's 
never used. I don't know if this is an issue with Chimera or with my 
machine, but I'll try to find out.

If you need any more info, please let me know.

Thank you for your help!


~Carlos Lopez


My system specs:
Mac Pro 4,1
     Mac OS X 10.6.3
     Quad-Core Intel Xeon, 2.66 GHz
     1 proc, 4 cores
     16 GB memory
Graphics Card
     NVIDIA GeForce GTX 285, VRAM total: 1024 MB
Chimera:
     Alpha version 1.5 build 30286 2010-03-23
     platform: darwin 64bit, windowing system: aqua