I have a situation in which I need to load a large number of separate
pdb files into a single pymol session. In this case, the number is
~150, but it could potentially be more. However, the amount of time
required to load a file appears to be strongly dependent on the number
of files already loaded. For example:
# of structures loaded time to load all structures (seconds)
5 0.82
10 2.49
20 11.05
30 29.85
40 62.48
50 115.25
60 189.79
70 302.67
80 432.82
90 589.23
unfortunately, this means that to load 150 structures takes over an
hour. I observe this behavior whether I am loading the structures all
at once using a python script, or one at a time. In both cases, I am
using the cmd.load() api function, but the built-in load command gives
similar results. The structures I am loading are (nearly) identical:
each has 263 residues (in a single chain); each individual pdb file is
about 215KB.
I am running this on a dual 2.0 GHz G5 system with 1.5 GB memory. The
long loading times are consistent between the two versions of pymol I
have installed: OSX/X11 hybrid version 0.97 and MacPyMol version 0.95.
During the long loading times, there is plenty of memory available, but
the processor load stays at 50% (i.e. one processor on my machine is
fully loaded throughout).
My gut feeling is that this situation should not be, but I don't yet
understand the structure of the code well enough to debug it. Can
anyone shed light on this issue?
Thanks in advance,
Ben Allen
