Re: [PyMOL] Reducing the surface rendering load for JSmol export
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 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- 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 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Reducing the surface rendering load for JSmol export
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 -- Nick Greevesvia 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:ngree...@liverpool.ac.ukmailto:ngree...@liverpool.ac.uk WWW Pages:http://www.chemtube3d.com Tel:+44 (0)151-794-3506 (3500 secretary) Dept Fax: +44 (0)151-794-3588 On 18 Jul 2013, at 10:12, pymol-users-requ...@lists.sourceforge.netmailto:pymol-users-requ...@lists.sourceforge.net wrote: Message: 6 Date: Thu, 18 Jul 2013 04:11:57 -0500 From: Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu Subject: Re: [PyMOL] Reducing the surface rendering load for JSmol export To: Thomas Holder thomas.hol...@schrodinger.commailto:thomas.hol...@schrodinger.com, pymol-users pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net Message-ID: CAF_YUvW2Vf1ucKbwX7trx-n81OEkGZ=0prdlb+_sc8jetur...@mail.gmail.commailto:CAF_YUvW2Vf1ucKbwX7trx-n81OEkGZ=0prdlb+_sc8jetur...@mail.gmail.com 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 -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] NVIDIA 3D error
I think I have tried all the solutions available. I continue to get: error: the requested 3d display mode is unavailable. I can run all the examples; apparently correctly. ASUS VG248 monitor NVIDIA quatro K600 video card NVIDIA 3D vision Suggestions? Dick -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
