From: Kilian B. <kil...@un...> - 2011-11-28 16:21:18
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Hi Nico, The wiki is available via http://<IP>/mediawiki/index.php/Main_Page I thought it should work, yes :-) I am more inclined to what Jaime mentioned - it seems that our wiki does not find the Jmol to execute - which is weird, as it gets the <jmol> tag. Thanks Kilian On 28 November 2011 15:50, Nicolas Vervelle <nve...@gm...> wrote: > Hi Kilian, > > The current Jmol extension under SVN should be working with MW 1.16 (it > works on Jmol wiki with MW 1.16.2). > The fix suggested by Jaime is indeed needed for MW 1.17 (but in line 827 > and others I believe). > > Can you confirm that your wiki is accessible through an URL looking like > http://xxxxx/mediawiki/ ? > > I will probably have some time available this weekend or the end of next > week to look into some problems. > > Nico > > > On Fri, Nov 25, 2011 at 10:58 AM, Kilian Baerwinkel < > kil...@un...> wrote: > >> Jaime, >> >> I can not access the Copyright test. >> >> But I am not sure I get your suggestion - the Jmol files are all in one >> directory "/extensions/Jmol", within the mediawiki directory, together with >> the mediawiki extension files. >> >> That being said, there is no directory named jmol-12.2.6... >> >> Best >> >> Kilian >> >> >> >> On 24 November 2011 20:41, Jaime Prilusky <jai...@we...>wrote: >> >>> Kilian, >>> >>> If you enter this URL on a browser (replace 'YourServerHere' with the >>> name of your server, localhost, etc), can you read the Copyright text? >>> >>> http://YouServerHere/mediawiki/extensions/Jmol/COPYRIGHT.txt >>> >>> If not, please either rename jmol-12.2.6 as Jmol or make a link/alias >>> as needed. >>> >>> Jaim >>> -- >>> Dr Jaime Prilusky >>> Head Bioinformatics >>> R&D Bioinformatics and Data Management >>> Department of Biological Services >>> Weizmann Institute of Science >>> 76100 Rehovot – Israel >>> >>> mail: Jai...@we... >>> tel: 972-8-9344959 >>> fax: 972-8-9344113 >>> >>> OCA, http://oca.weizmann.ac.il (the protein structure/function >>> database) >>> Proteopedia, http://proteopedia.org (because life has more than 2D) >>> >>> From: Kilian Baerwinkel <kil...@un...> >>> Reply-To: <jmo...@li...> >>> Date: Thu, 24 Nov 2011 18:34:12 +0100 >>> >>> To: <jmo...@li...> >>> Subject: Re: [Jmol-users] MediaWiki Plugin >>> >>> Hi, >>> >>> I am talking of the mediawiki extension, yes, the version is 3.3_dev. >>> >>> Also using: >>> >>> MediaWiki 1.16.5 >>> PHP 5.3.5-1ubuntu7.3 (apache2handler) >>> MySQL 5.1.54-1ubuntu4 >>> >>> >>> I have tested various versions of Jmol, at the moment I use 12.2.6 >>> (which is running all right for itself). >>> >>> On an empty page, there is the following code: >>> >>> <jmol> >>> <jmolApplet> >>> <size>150</size> >>> <inlineContents> >>> REMARK Butane >>> HETATM 1 C UNK 0 -0.769 0.000 0.000 C >>> HETATM 2 C UNK 0 0.769 0.000 0.000 C >>> HETATM 3 C UNK 0 -1.383 -0.728 1.203 C >>> HETATM 4 C UNK 0 1.382 -0.741 1.196 C >>> HETATM 5 H UNK 0 -1.127 1.059 0.007 H >>> HETATM 6 H UNK 0 -1.142 -0.461 -0.945 H >>> HETATM 7 H UNK 0 -1.001 -0.311 2.163 H >>> HETATM 8 H UNK 0 1.128 -0.488 -0.940 H >>> HETATM 9 H UNK 0 1.143 1.051 -0.017 H >>> HETATM 10 H UNK 0 -2.493 -0.625 1.206 H >>> HETATM 11 H UNK 0 -1.156 -1.818 1.183 H >>> HETATM 12 H UNK 0 2.492 -0.792 1.105 H >>> HETATM 13 H UNK 0 1.155 -0.230 2.158 H >>> HETATM 14 H UNK 0 1.000 -1.787 1.259 H >>> END >>> </inlineContents> >>> </jmolApplet> >>> </jmol> >>> >>> <jmolFile>MIL53_mimik_Loiseau.xyz</jmolFile> >>> >>> >>> >>> The source code of the page then shows this section, which I take for >>> the jmol part: >>> >>> <p><a href="javascript:void(0)" >>> onclick="jmolWikiPopupWindow('test.xyz','800','50','50','jmolInitialize(\'/mediawiki/extensions/Jmol\', >>> false); _jmol.noEval = true; jmolCheckBrowser(\'popup\', >>> \'/mediawiki/extensions/Jmol/browsercheck\', \'onclick\'); jmolApplet( 500, >>> \'set echo p 50% 50%;set echo p center;echo Loading...;refresh;load >>> /mediawiki/images/c/c9/test.xyz;\' ); ');">test.xyz</a></p> >>> <p><br><!-- Jmol --><script type="text/javascript"> >>> //<![CDATA[ >>> jmolInitialize('/mediawiki/extensions/Jmol', false); _jmol.noEval = >>> true; jmolCheckBrowser('popup', '/mediawiki/extensions/Jmol/browsercheck', >>> 'onclick');jmolSetAppletColor('black');jmolAppletInline(150, 'REMARK >>> Butane\nHETATM 1 C UNK 0 -0.769 0.000 0.000 >>> C\nHETATM 2 C UNK 0 0.769 0.000 0.000 >>> C\nHETATM 3 C UNK 0 -1.383 -0.728 1.203 >>> C\nHETATM 4 C UNK 0 1.382 -0.741 1.196 >>> C\nHETATM 5 H UNK 0 -1.127 1.059 0.007 H\nHETATM >>> 6 H UNK 0 -1.142 -0.461 -0.945 H\nHETATM 7 >>> H UNK 0 -1.001 -0.311 2.163 H\nHETATM 8 H UNK >>> 0 1.128 -0.488 -0.940 H\nHETATM 9 H UNK 0 >>> 1.143 1.051 -0.017 H\nHETATM 10 H UNK 0 >>> -2.493 -0.625 1.206 H\nHETATM 11 H UNK 0 >>> -1.156 -1.818 1.183 H\nHETATM 12 H UNK 0 2.492 -0.792 >>> 1.105 H\nHETATM 13 H UNK 0 1.155 -0.230 >>> 2.158 H\nHETATM 14 H UNK 0 1.000 -1.787 1.259 >>> H\nEND', ''); >>> //]]> >>> </script></p> >>> <p><br> >>> blubb</p> >>> >>> >>> Hope that helps. >>> >>> Best >>> >>> Kilian >>> >>> >>> On 24 November 2011 18:00, Jaime Prilusky <jai...@we... >>> > wrote: >>> >>>> Dear Angel, >>>> >>>> You are completely right in asking first more information on versions, >>>> before suggesting solutions :-) >>>> >>>> We are, at this time, testing the latest stable Jmol (12.2.6) with the >>>> latest stable MediaWiki (1.17.0) and found a problem similar to what >>>> Kilian described, so I suggested the fix that worked for us, without >>>> requesting additional details on Kilian configuration. >>>> >>>> I have not enough information as to say if this change should be made >>>> permanent, and what will happen if the 'fixed' Jmol extension is run on >>>> a >>>> previous MediaWiki version. What's clear is that some research is >>>> required. >>>> >>>> Best Regards, >>>> Jaim >>>> -- >>>> Dr Jaime Prilusky >>>> Head Bioinformatics >>>> R&D Bioinformatics and Data Management >>>> Department of Biological Services >>>> Weizmann Institute of Science >>>> 76100 Rehovot Israel >>>> >>>> mail: Jai...@we... >>>> tel: 972-8-9344959 >>>> fax: 972-8-9344113 >>>> >>>> OCA, http://oca.weizmann.ac.il (the protein structure/function >>>> database) >>>> Proteopedia, http://proteopedia.org (because life has more than 2D) >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 24/11/2011 6:27 PM, "Angel Herráez" <ang...@ua...> wrote: >>>> >>>> >Hi Jaime >>>> > >>>> >Do you think that is something that needs a permanent bug fix, or is >>>> >it just a per-case solution? >>>> > >>>> >El 24 Nov 2011 a las 13:34, Jaime Prilusky escribió: >>>> >> On line 833 of the file Jmol.body.php remove the '&' from the third >>>> >> parameter of the functionjmolTag() >>>> > >>>> > >>>> >>>> >-------------------------------------------------------------------------- >>>> >---- >>>> >All the data continuously generated in your IT infrastructure >>>> >contains a definitive record of customers, application performance, >>>> >security threats, fraudulent activity, and more. Splunk takes this >>>> >data and makes sense of it. IT sense. And common sense. >>>> >http://p.sf.net/sfu/splunk-novd2d >>>> >_______________________________________________ >>>> >Jmol-users mailing list >>>> >Jmo...@li... >>>> >https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> All the data continuously generated in your IT infrastructure >>>> contains a definitive record of customers, application performance, >>>> security threats, fraudulent activity, and more. Splunk takes this >>>> data and makes sense of it. IT sense. And common sense. >>>> http://p.sf.net/sfu/splunk-novd2d >>>> _______________________________________________ >>>> Jmol-users mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>> >>> >>> >>> >>> -- >>> ______ >>> >>> MSc. Chem. Kilian Bärwinkel >>> >>> Lehrstuhl für Anorganische Chemie I >>> Fakultät NW 1 >>> Universität Bayreuth >>> Universitätsstr. 30 >>> 95447 Bayreuth >>> >>> Tel: +49 921 55 - 4387 >>> Fax: +49 921 55 - 2788 >>> >>> e-mail: kil...@un... >>> >>> http://www.senker.uni-bayreuth.de >>> >>> ------------------------------------------------------------------------------ >>> All the data continuously generated in your IT infrastructure contains a >>> definitive record of customers, application performance, security threats, >>> fraudulent activity, and more. Splunk takes this data and makes sense of >>> it. IT sense. And common sense. >>> http://p.sf.net/sfu/splunk-novd2d_______________________________________________Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> ------------------------------------------------------------------------------ >>> All the data continuously generated in your IT infrastructure >>> contains a definitive record of customers, application performance, >>> security threats, fraudulent activity, and more. Splunk takes this >>> data and makes sense of it. IT sense. And common sense. >>> http://p.sf.net/sfu/splunk-novd2d >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >> >> >> -- >> ______ >> >> MSc. Chem. Kilian Bärwinkel >> >> Lehrstuhl für Anorganische Chemie I >> Fakultät NW 1 >> Universität Bayreuth >> Universitätsstr. 30 >> 95447 Bayreuth >> >> Tel: +49 921 55 - 4387 >> Fax: +49 921 55 - 2788 >> >> e-mail: kil...@un... >> >> http://www.senker.uni-bayreuth.de >> >> >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure >> contains a definitive record of customers, application performance, >> security threats, fraudulent activity, and more. Splunk takes this >> data and makes sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-novd2d >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- ______ MSc. Chem. Kilian Bärwinkel Lehrstuhl für Anorganische Chemie I Fakultät NW 1 Universität Bayreuth Universitätsstr. 30 95447 Bayreuth Tel: +49 921 55 - 4387 Fax: +49 921 55 - 2788 e-mail: kil...@un... http://www.senker.uni-bayreuth.de |