From: Miguel Howard <mth@mt...> - 2003-12-10 22:58:11
> By the way, I'm curious how well Jmol handles very large PDB files, such
> as the virus capids available in the Atlas (alpha carbon only, several
> megabytes; or all non-hydrogens, 50-100 megabytes) or large NMR
> ensembles (1JSA, 6 megs) compared to Chime.
I did a little testing of 1JSA.pdb in Jmol.
The file contains 24 models of +3000 atoms totalling 73368 atoms.
On my 1 Ghz Celeron Linux machine (3 years old) it takes 11 seconds to
load the file and display it.
5078 ms to load the file
1833 ms to 'autobond'
4381 ms to build the frame
With a screen size of approx 400x400 pixels:
With all 24 models/73K atoms displayed as wireframe it takes 200 ms to
render each frame during rotation.
With all 24models/73K atoms displayed as cpk 100% it take 400 ms to render
each frame during rotation
1 model 3056 atoms wireframe or cpk take 175 ms to render each frame
The trace and quasi-cartoon renderings look pretty good when applied to
all the models at the same time.
(For you computer hackers, note that 73K is more than 64K and 32K. So
while the Jmol code does use some short integers, they are not being used
in anything related to atom indices. Therefore, we shouldn't have any
'address-space' problems until we approach 2 billion atoms :-)
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