I'm currently using PyMol 1.4.1 on Ubuntu Linux 11.10. My hardware is fairly
up-to-date, an AMD 6-core, 3.2 GHz CPU ,and 4 GB of DDR1200 RAM. My only old
hardware is my NVidia 8800 GTS graphics card. I have started to assemble
rather large visualizations. I am noticing CPU performance lags, and
unexpectedly high memory usage. In my hands, PyMol is behaving like the
infamous Flash Player browser plug-in -- hogging memory and CPU cycles (as well
as disk space) for no obvious reason.
Here's an example. I have superimposed 15 PDB files which are snapshots from
GROMACS molecular dynamics simulations. These contain protein molecules in a
water box. I admit, the PDB files are pretty large, around 3.5 MB each.
Still, 15 x 3.5 MB = 52.5 MB. That should be manageable, I think. Ambitious,
but still within reasonable limits.
But what is the size of the PyMol session (.pse) file that I built from this
stack of PDB files? 234 MB! Why did this bloat up to fully five times the
size of the source data (which is already in plain text, and full of white
space)?
What's more, when I load this 234-MB file into PyMol, the Python interpreter
which PyMol invokes grabs a full 1.0 GB of memory. The CPU usage of that
Python interpreter (single-core, of course) immediately jumps to around 40%
even when I'm not asking PyMol to do anything. After I've worked with PyMol a
bit with this file loaded, CPU usage will jump to 100%, and it stays there.
Once that happens, the cursor will lag, jitter or freeze, and I can end up
selecting unintended menu items. Keep in mind, this is with a completely
stationary image in the PyMol Viewer window.
I'm looking to reduce all of this overhead. Excluding some water molecules
from the source PDB files comes to mind. Perhaps I can find a way to clip my
simulation box (I would like to retain the option to visualize any water
molecules which actually contact the protein). However, I seem to have more
fundamental problems than excess water molecules. Alternately, if there are
settings in PyMol that I can adjust to get it to behave, that would be great.
Thanks for any advice you may have!
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