Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Regarding updating the argument list for onBeforePageDisplay() to be just &$out -- PHP was satisfied but otherwise no change. Regarding your tests -- sorry I didn't include mention of purge tests from my end. But yes, our results matched: edit/preview ok, normal/live nok, purge ok. Now regarding your latest suggestion regarding disableCache() in wfJmolRender(), it's no dice on my end. I tried it together with our earlier edits up to and including above, and then I tried inserting the $wgParser->disableCache(); statement into a stock JmolExtension.php -- the results were the same (live nok). That includes Firefox 2.0.0.3 and IE7 with empty local caches, and after using the purge mode to clear MediaWiki's cache. Touching or otherwise updating MediaWiki's LocalSettings.php also forces MediaWiki to clear its cache, and I did so -- still nok on the live page. I was beginning to think this was a cache issue within MediaWiki and we could work around it with suitable tweaks to LocalSettings.php, now I don't know. All the test pages on wiki.jmol.org do work for me -- I think before today only the uploaded XYZ example worked properly, now all three upload examples work, as does the "Inlined CML File" example. FYI, I'm heading home for the day and won't be able to revisit this until Monday. Thanks for your attention and suggestions today, --JRM "Nicolas Vervelle" <[EMAIL PROTECTED]> 23-Mar-2007 19:06 To jmol-users@lists.sourceforge.net cc [EMAIL PROTECTED], [EMAIL PROTECTED] Subject Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page Bob Hanson wrote: Nicolas Vervelle wrote: If you can easily test modifications, I can try to help you with ideas to make the extension working. I have some problems with understanding the internal workings of MediaWiki, and this part is really difficult (finding how to include the links to Jmol javascript files only once per page, and only if the page is really using the Jmol extension). Nico -- note that now with the automatic initialization, in the MediaWiki business you would not do the initialization at all, and that at least takes care of the problem that you might have 0 or multiple initializations. Ok, that could help but I am also trying to include Jmol.js only once by putting the
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Nicolas Vervelle wrote: > If you can easily test modifications, I can try to help you with ideas > to make the extension working. > I have some problems with understanding the internal workings of > MediaWiki, and this part is really difficult (finding how to include > the links to Jmol javascript files only once per page, and only if the > page is really using the Jmol extension). Nico -- note that now with the automatic initialization, in the MediaWiki business you would not do the initialization at all, and that at least takes care of the problem that you might have 0 or multiple initializations. > To easily test on my side, I need to setup a wiki on my computer > rather than using Jmol wiki, and it requires some time. > > An other idea to make it work is to use the BeforePageDisplay hook. > Try the following : > - like the onParserAfterScript() function, create a > onBeforePageDisplay() function with the same content, using the > modified version of the "if". > - in the wfJmolExtension() function, comment out the > "$wgHooks['ParserAfterStrip'][] = $wgJmolExtension;" line and add a > new line "$wgHooks['BeforePageDisplay'][] = $wgJmolExtension;" line > > Tell me if you have better result > It may require purging the page to have the modification taken into > account (use the purge action: go into edit mode, and replace edit by > purge in the URL). > > Nico > > [EMAIL PROTECTED] wrote: > >> >> Hi Nico. Changed line 576 as you suggested, but no joy -- the >> behavior is the same. >> >> --JRM >> >> Hi, >> >> Since several months, I have a lot of work and didn't get the courage of >> working again on the Jmol extension. >> I think a simple fix should be the following : in function >> onParserAfterStrip(), try replacing the "if ($this->mJmolTagPresent == >> true) {" line by "if (true) {". >> >> Tell me if it works ... >> >> Nico >> >> [EMAIL PROTECTED] wrote: >> > >> > Hi folks. I support a small internal wiki for group use within my >> > company. Recently a chemist inquired about embedding Jmol within a >> > wiki page, and I found the Jmol MediaWiki extension: >> > >> > http://wiki.jmol.org:81/index.php/MediaWiki >> > >> > I installed the extension according to the instructions and found >> > that, while I can get the Jmol applet to display properly in the >> > wiki's "Show Preview" mode while editing the page, viewing the live >> > page gets no applet at all. It seems the Javacript lines to include >> > Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being >> > included in the live page. This is with Jmol 11.0.1 and MediaWiki >> > 1.7.1. I think my problem is similar to Kevin Murphy's situation, >> > posted here on 2007-01-23: >> > >> > >> http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html >> >> > >> > >> > I couldn't find a resolution in the list archive. Is this a problem >> > within the Jmol extension, or MediaWiki itself? I'd appreciate any >> > suggestions and am willing to test tweaks to the extension. Thanks, >> > >> > --JRM >> > >> >> > >> > >> - >> > Take Surveys. Earn Cash. Influence the Future of IT >> > Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> > opinions on IT & business topics through brief surveys-and earn cash >> > >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> > >> >> > >> > ___ >> > Jmol-users mailing list >> > Jmol-users@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/jmol-users >> > >> >> >> >> >> >>- >>Take Surveys. Earn Cash. Influence the Future of IT >>Join SourceForge.net's Techsay panel and you'll get the chance to share your >>opinions on IT & business topics through brief surveys-and earn cash >>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> >> >> >>___ >>Jmol-users mailing list >>Jmol-users@lists.sourceforge.net >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > >- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys-and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > >-
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
I have managed to set up a local wiki for testing. Here's what I see : - in edit mode: ok - in normal mode: nok - in purge mode (replace edit by purge in the edit mode URL): ok I am going to try to find help on the Mediawiki irc channel Nico [EMAIL PROTECTED] wrote: Okay, so the resulting diff on JmolExtension.php is as follows. No change, aside from PHP complaining about not having a second argument to pass to onBeforePageDisplay(). Incidentally I do have $wgAllowUserCss = true and $wgAllowUserJs = true in MediaWiki's LocalSettings.php to encourage the wiki not to strip out any contributed _javascript_ or CSS, though I'd think the wiki would consider code coming from an extension as being non-user in origin. --JRM 586a587,601 > > // Experimental callback called before display > function onBeforePageDisplay(&$parser, &$text, &$x) { > global $wgJmolExtensionPath,$wgOut; > if (true) { > $this->includeScript($wgOut, $wgJmolExtensionPath."/Jmol.js"); > $this->includeScript($wgOut, $wgJmolExtensionPath."/JmolMediaWiki.js"); > if ($this->mValSigned) { > $this->addScript($wgOut, "jmolInitialize('".$wgJmolExtensionPath."', true);"); > } else { > $this->addScript($wgOut, "jmolInitialize('".$wgJmolExtensionPath."', false);"); > } > } > $this->mJmolTagPresent = false; > } 606c621,622 < $wgHooks['ParserAfterStrip'][] = $wgJmolExtension; --- > // $wgHooks['ParserAfterStrip'][] = $wgJmolExtension; > $wgHooks['BeforePageDisplay'][] = $wgJmolExtension; "Nicolas Vervelle" <[EMAIL PROTECTED]> 23-Mar-2007 16:34 To jmol-users@lists.sourceforge.net cc [EMAIL PROTECTED] Subject Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page If you can easily test modifications, I can try to help you with ideas to make the extension working. I have some problems with understanding the internal workings of MediaWiki, and this part is really difficult (finding how to include the links to Jmol _javascript_ files only once per page, and only if the page is really using the Jmol extension). To easily test on my side, I need to setup a wiki on my computer rather than using Jmol wiki, and it requires some time. An other idea to make it work is to use the BeforePageDisplay hook. Try the following : - like the onParserAfterScript() function, create a onBeforePageDisplay() function with the same content, using the modified version of the "if". - in the wfJmolExtension() function, comment out the "$wgHooks['ParserAfterStrip'][] = $wgJmolExtension;" line and add a new line "$wgHooks['BeforePageDisplay'][] = $wgJmolExtension;" line Tell me if you have better result It may require purging the page to have the modification taken into account (use the purge action: go into edit mode, and replace edit by purge in the URL). Nico [EMAIL PROTECTED] wrote: Hi Nico. Changed line 576 as you suggested, but no joy -- the behavior is the same. --JRM Hi, Since several months, I have a lot of work and didn't get the courage of working again on the Jmol extension. I think a simple fix should be the following : in function onParserAfterStrip(), try replacing the "if ($this->mJmolTagPresent == true) {" line by "if (true) {". Tell me if it works ... Nico [EMAIL PROTECTED] wrote: > > Hi folks. I support a small internal wiki for group use within my > company. Recently a chemist inquired about embedding Jmol within a > wiki page, and I found the Jmol MediaWiki extension: > > http://wiki.jmol.org:81/index.php/MediaWiki > > I installed the extension according to the instructions and found > that, while I can get the Jmol applet to display properly in the > wiki's "Show Preview" mode while editing the page, viewing the live > page gets no applet at all. It seems the Javacript lines to include > Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being > included in the live page. This is with Jmol 11.0.1 and MediaWiki > 1.7.1. I think my problem is similar to Kevin Murphy's situation, > posted here on 2007-01-23: > > http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html > > > I couldn't find a resolution in the list archive. Is thi
Re: [Jmol-users] redesigning Jmol.org website main menu
Good ideas Angel, here is a suggestion: Home Demonstration pages Screenshots Demonstration pages how about changing this second occurrence of "demonstration pages" to "applet demonstrations" or something else indicating live applet? Frieda - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Okay, so the resulting diff on JmolExtension.php is as follows. No change, aside from PHP complaining about not having a second argument to pass to onBeforePageDisplay(). Incidentally I do have $wgAllowUserCss = true and $wgAllowUserJs = true in MediaWiki's LocalSettings.php to encourage the wiki not to strip out any contributed JavaScript or CSS, though I'd think the wiki would consider code coming from an extension as being non-user in origin. --JRM 586a587,601 > > // Experimental callback called before display > function onBeforePageDisplay(&$parser, &$text, &$x) { > global $wgJmolExtensionPath,$wgOut; > if (true) { > $this->includeScript($wgOut, $wgJmolExtensionPath."/Jmol.js"); > $this->includeScript($wgOut, $wgJmolExtensionPath."/JmolMediaWiki.js"); > if ($this->mValSigned) { > $this->addScript($wgOut, "jmolInitialize('".$wgJmolExtensionPath."', true);"); > } else { > $this->addScript($wgOut, "jmolInitialize('".$wgJmolExtensionPath."', false);"); > } > } > $this->mJmolTagPresent = false; > } 606c621,622 < $wgHooks['ParserAfterStrip'][] = $wgJmolExtension; --- > // $wgHooks['ParserAfterStrip'][] = $wgJmolExtension; > $wgHooks['BeforePageDisplay'][] = $wgJmolExtension; "Nicolas Vervelle" <[EMAIL PROTECTED]> 23-Mar-2007 16:34 To jmol-users@lists.sourceforge.net cc [EMAIL PROTECTED] Subject Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page If you can easily test modifications, I can try to help you with ideas to make the extension working. I have some problems with understanding the internal workings of MediaWiki, and this part is really difficult (finding how to include the links to Jmol javascript files only once per page, and only if the page is really using the Jmol extension). To easily test on my side, I need to setup a wiki on my computer rather than using Jmol wiki, and it requires some time. An other idea to make it work is to use the BeforePageDisplay hook. Try the following : - like the onParserAfterScript() function, create a onBeforePageDisplay() function with the same content, using the modified version of the "if". - in the wfJmolExtension() function, comment out the "$wgHooks['ParserAfterStrip'][] = $wgJmolExtension;" line and add a new line "$wgHooks['BeforePageDisplay'][] = $wgJmolExtension;" line Tell me if you have better result It may require purging the page to have the modification taken into account (use the purge action: go into edit mode, and replace edit by purge in the URL). Nico [EMAIL PROTECTED] wrote: Hi Nico. Changed line 576 as you suggested, but no joy -- the behavior is the same. --JRM Hi, Since several months, I have a lot of work and didn't get the courage of working again on the Jmol extension. I think a simple fix should be the following : in function onParserAfterStrip(), try replacing the "if ($this->mJmolTagPresent == true) {" line by "if (true) {". Tell me if it works ... Nico [EMAIL PROTECTED] wrote: > > Hi folks. I support a small internal wiki for group use within my > company. Recently a chemist inquired about embedding Jmol within a > wiki page, and I found the Jmol MediaWiki extension: > > http://wiki.jmol.org:81/index.php/MediaWiki > > I installed the extension according to the instructions and found > that, while I can get the Jmol applet to display properly in the > wiki's "Show Preview" mode while editing the page, viewing the live > page gets no applet at all. It seems the Javacript lines to include > Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being > included in the live page. This is with Jmol 11.0.1 and MediaWiki > 1.7.1. I think my problem is similar to Kevin Murphy's situation, > posted here on 2007-01-23: > > http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html > > > I couldn't find a resolution in the list archive. Is this a problem > within the Jmol extension, or MediaWiki itself? I'd appreciate any > suggestions and am willing to test tweaks to the extension. Thanks, > > --JRM > > > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay pan
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
If you can easily test modifications, I can try to help you with ideas to make the extension working. I have some problems with understanding the internal workings of MediaWiki, and this part is really difficult (finding how to include the links to Jmol _javascript_ files only once per page, and only if the page is really using the Jmol extension). To easily test on my side, I need to setup a wiki on my computer rather than using Jmol wiki, and it requires some time. An other idea to make it work is to use the BeforePageDisplay hook. Try the following : - like the onParserAfterScript() function, create a onBeforePageDisplay() function with the same content, using the modified version of the "if". - in the wfJmolExtension() function, comment out the "$wgHooks['ParserAfterStrip'][] = $wgJmolExtension;" line and add a new line "$wgHooks['BeforePageDisplay'][] = $wgJmolExtension;" line Tell me if you have better result It may require purging the page to have the modification taken into account (use the purge action: go into edit mode, and replace edit by purge in the URL). Nico [EMAIL PROTECTED] wrote: Hi Nico. Changed line 576 as you suggested, but no joy -- the behavior is the same. --JRM Hi, Since several months, I have a lot of work and didn't get the courage of working again on the Jmol extension. I think a simple fix should be the following : in function onParserAfterStrip(), try replacing the "if ($this->mJmolTagPresent == true) {" line by "if (true) {". Tell me if it works ... Nico [EMAIL PROTECTED] wrote: > > Hi folks. I support a small internal wiki for group use within my > company. Recently a chemist inquired about embedding Jmol within a > wiki page, and I found the Jmol MediaWiki extension: > > http://wiki.jmol.org:81/index.php/MediaWiki > > I installed the extension according to the instructions and found > that, while I can get the Jmol applet to display properly in the > wiki's "Show Preview" mode while editing the page, viewing the live > page gets no applet at all. It seems the Javacript lines to include > Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being > included in the live page. This is with Jmol 11.0.1 and MediaWiki > 1.7.1. I think my problem is similar to Kevin Murphy's situation, > posted here on 2007-01-23: > > http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html > > > I couldn't find a resolution in the list archive. Is this a problem > within the Jmol extension, or MediaWiki itself? I'd appreciate any > suggestions and am willing to test tweaks to the extension. Thanks, > > --JRM > > > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] redesigning Jmol.org website main menu
Hi Angel, I would say: go with your changes :) Remodelling the menu is a good idea. Rather than implementing redirection pages, you could simply add redirects in the .htaccess file (there's an example for redirecting http://www.jmol.org/files to the sourceforge download page) Nico Angel Herraez wrote: Hello all I think the top-right menu of links at jmol.org is getting complex, and I have a couple of ideas for remodelling it, on which I would like opinions: We have "History" and "Changes", and "News" has just been proposed by Bob (a link to SourceForge News page for Jmol) I propose to join them all under a single entry. "Documentation", "Interactive Scripting Doc", "_javascript_ Library", "Colors", "Tech notes" could be joined in a single "Documentation" entry [ Caveat: these changes may break links from outside. I could take care of that implementing (temporary) redirection pages. ] Something like this (first-level entries would be menu links, second level would be sub-entries within content of the respective pages): Home Demonstration pages Screenshots Demonstration pages Simple sample pages Websites Documentation The Jmol Guide (link) The Jmol Applet Guide (link) Interactive Scripting Documentation (link) Surface Documentation (link) Jmol.js _javascript_ Library Colors The Jmol Developers Guide (link) Tech notes Jmol Literature (link) Wiki (link) History News (link) The origins of Jmol Jmol grows Jmol - an open source replacement for the Chime plugin Changes Contributors Browser Check FAQs Download Project pages Mailing lists SF Project page (link) Bug Database (link) Feature Requests (link) - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Hi Nico. Changed line 576 as you suggested, but no joy -- the behavior is the same. --JRM "Nicolas Vervelle" <[EMAIL PROTECTED]> 23-Mar-2007 15:33 To jmol-users@lists.sourceforge.net cc [EMAIL PROTECTED] Subject Re: [Jmol-users] Jmol MediaWiki extension, works in preview but not on live page Hi, Since several months, I have a lot of work and didn't get the courage of working again on the Jmol extension. I think a simple fix should be the following : in function onParserAfterStrip(), try replacing the "if ($this->mJmolTagPresent == true) {" line by "if (true) {". Tell me if it works ... Nico [EMAIL PROTECTED] wrote: > > Hi folks. I support a small internal wiki for group use within my > company. Recently a chemist inquired about embedding Jmol within a > wiki page, and I found the Jmol MediaWiki extension: > > http://wiki.jmol.org:81/index.php/MediaWiki > > I installed the extension according to the instructions and found > that, while I can get the Jmol applet to display properly in the > wiki's "Show Preview" mode while editing the page, viewing the live > page gets no applet at all. It seems the Javacript lines to include > Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being > included in the live page. This is with Jmol 11.0.1 and MediaWiki > 1.7.1. I think my problem is similar to Kevin Murphy's situation, > posted here on 2007-01-23: > > http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html > > > I couldn't find a resolution in the list archive. Is this a problem > within the Jmol extension, or MediaWiki itself? I'd appreciate any > suggestions and am willing to test tweaks to the extension. Thanks, > > --JRM > > > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] redesigning Jmol.org website main menu
Hello all I think the top-right menu of links at jmol.org is getting complex, and I have a couple of ideas for remodelling it, on which I would like opinions: We have "History" and "Changes", and "News" has just been proposed by Bob (a link to SourceForge News page for Jmol) I propose to join them all under a single entry. "Documentation", "Interactive Scripting Doc", "_javascript_ Library", "Colors", "Tech notes" could be joined in a single "Documentation" entry [ Caveat: these changes may break links from outside. I could take care of that implementing (temporary) redirection pages. ] Something like this (first-level entries would be menu links, second level would be sub-entries within content of the respective pages): Home Demonstration pages Screenshots Demonstration pages Simple sample pages Websites Documentation The Jmol Guide (link) The Jmol Applet Guide (link) Interactive Scripting Documentation (link) Surface Documentation (link) Jmol.js _javascript_ Library Colors The Jmol Developers Guide (link) Tech notes Jmol Literature (link) Wiki (link) History News (link) The origins of Jmol Jmol grows Jmol - an open source replacement for the Chime plugin Changes Contributors Browser Check FAQs Download Project pages Mailing lists SF Project page (link) Bug Database (link) Feature Requests (link) - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] help
Hi Vivi In principle, you include the path together with the filename: jmolApplet(350,"load /whatever/path/is_your_file/S_0003_8934_0001.pdb"); However, using absolute paths is delicate, due to Java security restrictions. That will only work from web server, not from local file. Make sure to read a summary at http://jmol.sourceforge.net/jslibrary/index.en.html#General%20Recommendations - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol MediaWiki extension, works in preview but not on live page
Hi folks. I support a small internal wiki for group use within my company. Recently a chemist inquired about embedding Jmol within a wiki page, and I found the Jmol MediaWiki extension: http://wiki.jmol.org:81/index.php/MediaWiki I installed the extension according to the instructions and found that, while I can get the Jmol applet to display properly in the wiki's "Show Preview" mode while editing the page, viewing the live page gets no applet at all. It seems the Javacript lines to include Jmol.js and JmolMediaWiki.js and call JmolInitialize() are not being included in the live page. This is with Jmol 11.0.1 and MediaWiki 1.7.1. I think my problem is similar to Kevin Murphy's situation, posted here on 2007-01-23: http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg07674.html I couldn't find a resolution in the list archive. Is this a problem within the Jmol extension, or MediaWiki itself? I'd appreciate any suggestions and am willing to test tweaks to the extension. Thanks, --JRM- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] help
Hi, Now I have a question about how to use the "load" method to load a file. I use this method like tihs in HTML: . jmolApplet(350,"load S_0003_8934_0001.pdb"); but if the S_0003_8934_0001.pdb and the HTML file are not in the same path, How can I use this command? I want to use the absolute path ,because the path includes the session in it. Thank you very much! Vivi - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] two more minor issues
Using jmol 11.1.25: * When rendering long thin structures in povray, jmol builds a gigantic empty boundary around the structure. This is not the case for direct jpg export. Somehow the boundary defaults for povray do not match the jmol window at all. I can provide an example if necessary. * With white background, displayed labels (e.g. atom numbers) for hydrogen are also white and hence unreadable by default. [I am sure this happens for other elements with other backgrounds]. Perhaps the default could be changed based on the current background color? best, VB - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [jmol-users] showing 2 models from different files
Please don't recommend the "1001 1002" business --- that was a transient idea that is still there, but will be dropped from the documentation, as it is not fully generalizable. display */1001 or */2001 display */1001, */2001 restrict */1001 or */2001 select */1001 or */2001; display selected should now read: display */1.1 or */2.1 display */1.1, */2.1 restrict */1.1 or */2.1 select */1.1 or */2.1; display selected For all models in a given file, use ".0" display */2.0 for example. Angel Herraez wrote: >Hi Jochen > >I'm not an expert in multi-frame models, and hence not sure if what >you tried should work, but try these other ways: > > display */1001 or */2001 > display */1001, */2001 > restrict */1001 or */2001 > select */1001 or */2001; display selected > > >Anyway, new syntax recommended in Jmol 11.1 is file nr.-dot-model >nr.: > display */1.1 or */2.1 > >There are several recent posts regarding this in the users list > > >- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys-and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [jmol-users] showing 2 models from different files
Hi Jochen I'm not an expert in multi-frame models, and hence not sure if what you tried should work, but try these other ways: display */1001 or */2001 display */1001, */2001 restrict */1001 or */2001 select */1001 or */2001; display selected Anyway, new syntax recommended in Jmol 11.1 is file nr.-dot-model nr.: display */1.1 or */2.1 There are several recent posts regarding this in the users list - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] [jmol-users] showing 2 models from different files
Hello everybody, I have a problem again. I've loaded two files into my applet with: load "fileset" "file1" "file2" Now i want to show models from the two files at the same time. I've tested model 1001 or 2001 frame 1001 or frame 2001 and so on. Nothing worked. How can i deal with it. Thanks for help Jochen - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users