From: <lsp...@we...> - 2009-01-30 05:42:27
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Hi, Is there a way to reduce the time required for Jmol for generating and rendering surfaces? Can we optimize the script data to help Jmol, ie: store the coordinates in the script on a better order, select atoms in a better way, pre-calculate something ? Thanks in advance, Jaim -- Dr Jaime Prilusky | Jai...@we... Head of Bioinformatics ISPC | R&D Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://www.proteopedia.org (because life has more than 2D) ------------------------------------------------------------------------ |
From: Angel H. <ang...@ua...> - 2009-01-30 10:36:23
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Jaime, I was writing a post for the Proteopedia list explaining just this. Here is my advice: I haven't looked at the source code, but this may help: the sensible thing for pre-programmed surfaces in web pages is to have Jmol save them as jvxl files, then make the page load that file - - much faster than calculating it every time. Also, I would add a message inside Jmol itself while the model loads. It is discouraging to have a white empty square. See http://wiki.jmol.org/index.php/Recycling_Corner#Providing_a_.27please_ wait.27_notice_while_the_applet_loads You could also add a warning (using echo) while the surface is calculated or loaded. A typo: "of the hemes by toogling off the spin" should be "toggling", right? |
From: <lsp...@we...> - 2009-02-01 11:17:45
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According to "Angel Herraez" <ang...@ua...>: > I haven't looked at the source code, but this may help: > the sensible thing for pre-programmed surfaces in web pages is to > have Jmol save them as jvxl files, then make the page load that file - > - much faster than calculating it every time. > Also, I would add a message inside Jmol itself while the model loads. > It is discouraging to have a white empty square. See > http://wiki.jmol.org/index.php/Recycling_Corner#Providing_a_.27please_ > wait.27_notice_while_the_applet_loads Thanks Angel for the suggestions, Jaim -- Dr Jaime Prilusky | Jai...@we... Head of Bioinformatics ISPC | R&D Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://www.proteopedia.org (because life has more than 2D) ------------------------------------------------------------------------ |
From: Karl O. <obe...@me...> - 2009-01-30 13:52:41
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In settings other than Proteopedia I reduce the time required to display a surface by generating a data file of the surface, and then just display the surface rather than calculate the surface each time the script is run. I do not think that there is a way to do this in Proteopedia, at least I have not discovered how to do it if it is possible. Karl >>> <lsp...@we...> 1/30/2009 12:21 AM >>> Hi, Is there a way to reduce the time required for Jmol for generating and rendering surfaces? Can we optimize the script data to help Jmol, ie: store the coordinates in the script on a better order, select atoms in a better way, pre-calculate something ? Thanks in advance, Jaim -- Dr Jaime Prilusky | Jai...@we... Head of Bioinformatics ISPC | R&D Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il ( http://oca.weizmann.ac.il/ ) (the protein structure/function database) Proteopedia, http://www.proteopedia.org ( http://www.proteopedia.org/ ) (because life has more than 2D) ------------------------------------------------------------------------ ------------------------------------------------------------------------------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Robert H. <ha...@st...> - 2009-01-30 14:35:48
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Jaim, I also suggest using write isosurface "xxxx.jvxl" from the Jmol application or signed applet. This only works if you have a predefined notion of the surface you want to display; see notes at http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm and http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf Basically, you just create the surface and write it to disk, then load it with the isosurface command: isosurface "xxxx.jvxl" Bob On Fri, Jan 30, 2009 at 7:52 AM, Karl Oberholser <obe...@me...> wrote: > In settings other than Proteopedia I reduce the time required to display a > surface by generating a data file of the surface, and then just display the > surface rather than calculate the surface each time the script is run. I do > not think that there is a way to do this in Proteopedia, at least I have not > discovered how to do it if it is possible. > > Karl > >>>> <lsp...@we...> 1/30/2009 12:21 AM >>> > Hi, > > Is there a way to reduce the time required for Jmol for generating > and rendering surfaces? > > Can we optimize the script data to help Jmol, ie: store the coordinates in > the script on a better order, select atoms in a better way, pre-calculate > something ? > > Thanks in advance, > Jaim > -- > Dr Jaime Prilusky | Jai...@we... > Head of Bioinformatics ISPC | > R&D Bioinformatics and Data Management | > Weizmann Institute of Science | fax: 972-8-9344113 > 76100 Rehovot - Israel | tel: 972-8-9344959 > > OCA, http://oca.weizmann.ac.il (the protein structure/function database) > Proteopedia, http://www.proteopedia.org (because life has more than 2D) > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 |
From: <lsp...@we...> - 2009-02-01 11:18:40
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According to "Robert Hanson" <ha...@st...>: > write isosurface "xxxx.jvxl" > http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm > http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf > isosurface "xxxx.jvxl" Thanks Bob for the suggestions, examples and reference, Jaim -- Dr Jaime Prilusky | Jai...@we... Head of Bioinformatics ISPC | R&D Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://www.proteopedia.org (because life has more than 2D) ------------------------------------------------------------------------ |