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 <> 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"


Greeves, Nick wrote, On 07/16/13 07:56:
>> I am interested in displaying PyMOL session files using 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

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