spacefill is not what you think. It is extremely fast. No "ball" is ever
created, and no "resolution" is even conceivable. A "spacefill" is simply a
line of ones and zeros that is cached in memory.
We see some significant browser issues with JSmol with large protein models
from any source. You have to consider that from any source, not just PyMOL.
Surfaces in particular are challenging, especially in Safari, which appears
to generally run much slower than Firefox, presumably because Apple has not
invested in optimizing its JavaScript.
However, here's a thought: My experience with PyMOL models is that the user
can get rather "lazy" and have all sorts of duplications that are
unnecessary. Jmol may load 100,000 atoms and create multiple surfaces when
only 20,000 and one surface are actually currently visible, for instance.
So if the PyMOL model is yours to start with, you might think about
deleting unnecessary PyMOL objects (listed on the right in PyMOL) before
taking the model to Jmol.
There is an interesting flag -- sorry that none of this is documented yet,
that's one of my next tasks ---
FILTER "nosurface"
that does a fast load without any surfaces. You might consider that. In
addition, then
FILTER "docache"
option may be of help. If you do that, then IMMEDIATELY upon reading the
PyMOL file, issue
WRITE PNGJ "filenameHere.png"
Then load that PNG file using
script "filenameHere.png"
This will create a file that should load much faster and render surfaces
much faster (though still requiring some time, of course).
Please do contribute your files to our growing practice set -- send a zip
file of them to Jaime Prilusky <[email protected]> -- so that
we can have more test files.
Bob
On Tue, Jul 16, 2013 at 11:17 PM, Greeves, Nick <[email protected]>wrote:
> I have a series of models that originate in PyMOL and load nicely
> into Jmol.jar. I would like to display them using JSMol and am seeing very
> slow loading times and slow response on mouse movement.
>
> I think I can speed up the cartoon based aspects using set hermiteLevel, set
> highResolution OFF and related commands but I would also like to display
> space-filling models.
>
> I have not been able to locate commands to reduce the detail/smoothness
> of space filling.
>
> Are there any commands that speed up the display of space filling models
> containing 34000 atoms?
>
> Best regards
> Nick
> --
> Nick Greeves via OS X Mail
> Director of Teaching and Learning
> Department of Chemistry
> University of Liverpool
> Donnan and Robert Robinson Laboratories
>
> Crown Street, LIVERPOOL L69 7ZD U.K.
> Email address: [email protected]
> WWW Pages: http://www.chemtube3d.com
> Tel: +44 (0)151-794-3506 (3500 secretary)
> Dept Fax: +44 (0)151-794-3588
>
>
>
>
>
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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