Nick, if these are just molecular surfaces, there is nothing to do in
PyMOL. The PSE files have only an indication of which atoms to create the
surface for, not the surface itself. Jmol/JSmol reads the PSE files
directly, determines what molecular surface to create, and uses its own
algorithms. Right now the import doesn't give an option for a default
resolution, but we could adapt that if needed. You are right that the
generation of surfaces is the bottleneck in a JavaScript-only solution.
I'll be documenting the "doCache" load option for PSE files soon, which
allows you to convert surfaces to a JVXL format and include them in PNGJ
files for better delivery over the web. It's a work in progress...
Bob Hanson
On Wed, Jul 17, 2013 at 2:29 AM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> Hi Nick,
>
> did you try the "surface_quality" setting? The default value is 0.
> That's for molecular surfaces.
>
> PyMOL> set surface_quality, -1
>
> The resolution of isosurfaces is determined by the resolution of the map
> as far as I know. You can reduce the map resolution with the "map_halve"
> command.
>
> Cheers,
> Thomas
>
> Greeves, Nick wrote, On 07/16/13 07:56:
> >> I am interested in displaying PyMOL session files using JSmol
> >> http://sourceforge.net/projects/jsmol/ Basically this works but some
> >> of the session files have high resolution surfaces which put a
> >> tremendous strain on JSmol/browser when they are displayed.
> >>
> >> I am new to PyMOL and cannot see how to adjust the settings to produce
> >> a lower resolution surface in PyMOL that should work better in JSmol.
> >> I have tried all the menus and looked at all the settings without
> success.
> >>
> >> Any advice would be most welcome.
> >> Best regards
> >> Nick
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
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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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