Thanks Thomas and Bob,

I had tried surface_quality with little effect.

The "doCACHE" option does indeed shrink the files which make the web transfer faster but then JSmol still has to work very hard to render the large molecules and their surfaces. Once loaded the generation of molecular surfaces using spacefill is fast. For the moment we will stick with Jmol (and Java) just for those pages because it is so much faster and the PyMOL to Jmol conversion works so beautifully. 

It is easy to switch back to Java-free JSmol as it progresses (usually very quickly).

Best regards
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:
WWW Pages: 
Tel:            +44 (0)151-794-3506 (3500 secretary)
Dept Fax:   +44 (0)151-794-3588

On 18 Jul 2013, at 10:12, wrote:

Message: 6
Date: Thu, 18 Jul 2013 04:11:57 -0500
From: Robert Hanson <>
Subject: Re: [PyMOL] Reducing the surface rendering load for JSmol
To: Thomas Holder <>,  pymol-users
Content-Type: text/plain; charset="iso-8859-1"

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