[Chimera-users] Virus Capsid Reconstruction--Slow Performance
karkis77 at gmail.com
Thu May 27 13:58:08 PDT 2010
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
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!
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
NVIDIA GeForce GTX 285, VRAM total: 1024 MB
Alpha version 1.5 build 30286 2010-03-23
platform: darwin 64bit, windowing system: aqua
More information about the Chimera-users