Hi Nico,
I have also tried less complex tags like <jmolPdb>1ALE</jmolPdb>,
<jmolfile>. Both display a blue link in hte wiki, but nothing happens if
the link is clicked.
Jaime,
all the files are accessible for the servers user, both owner and
permissions are the same as for other extensions, which are working.
Best
Kilian
On 29 November 2011 10:06, Nicolas Vervelle <nverve...@gmail.com> wrote:
> Hi Kilian,
>
> Can you also try the simpler tags ?
> There are 2 sets of tags :
>
> - a complex one, <jmol>, which can be used to customize a lot of things
> - several simpler tags, <jmolFile>, <jmolPdb>, <jmolSmiles>, which
> have been added later to provide a simple interface for users
>
> Nico
>
> On Mon, Nov 28, 2011 at 5:21 PM, Kilian Baerwinkel <
> kilian.baerwin...@uni-bayreuth.de> wrote:
>
>> 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 <nverve...@gmail.com> 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 <
>>> kilian.baerwin...@uni-bayreuth.de> 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 <
>>>> jaime.prilu...@weizmann.ac.il> 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: jaime.prilu...@weizmann.ac.il
>>>>> 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 <kilian.baerwin...@uni-bayreuth.de>
>>>>> Reply-To: <jmol-users@lists.sourceforge.net>
>>>>> Date: Thu, 24 Nov 2011 18:34:12 +0100
>>>>>
>>>>> To: <jmol-users@lists.sourceforge.net>
>>>>> 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 <
>>>>> jaime.prilu...@weizmann.ac.il> 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: jaime.prilu...@weizmann.ac.il
>>>>>> 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" <angel.herr...@uah.es> 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
>>>>>> >Jmol-users@lists.sourceforge.net
>>>>>> >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
>>>>>> Jmol-users@lists.sourceforge.net
>>>>>> 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: kilian.baerwin...@uni-bayreuth.de
>>>>>
>>>>> 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
>>>>> Jmol-users@lists.sourceforge.net
>>>>> 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
>>>>> Jmol-users@lists.sourceforge.net
>>>>> 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: kilian.baerwin...@uni-bayreuth.de
>>>>
>>>> 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
>>>> Jmol-users@lists.sourceforge.net
>>>> 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
>>> Jmol-users@lists.sourceforge.net
>>> 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: kilian.baerwin...@uni-bayreuth.de
>>
>> 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
>> Jmol-users@lists.sourceforge.net
>> 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
> Jmol-users@lists.sourceforge.net
> 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: kilian.baerwin...@uni-bayreuth.de
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
