Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
On 2 Mar 2012, at 16:54, Robert Hanson wrote: Well, then I propose /*file*/ within a script is adapted by MediaWiki to change that to a proper file name. On Fri, Mar 2, 2012 at 9:51 AM, Nicolas Vervelle nverve...@gmail.comwrote: an alternative which by-passes the file path naming problem is to load everything into a .jmol file, as suggested by Angel (thanks!). This can appear in the Wiki as a link jmolFile text=just a linkAHB_mo22.cub.jmol/jmolFile (I have created this page for my students' use; http://www.ch.imperial.ac.uk/rzepa/cub2jvxl/ ) There is an issue with surface colours that we are looking at (if anyone can spot a fix, do please let me know). -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
My point was that if MediaWiki would just insert the Jmol script code for defaultDirectory in the startup script, then the user can include numerous files with no prefix and no concern over where they are. Bob -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
I have the impression that I'm missing a point in this discussion... The situation Henry is talking about is that he need to access several files that have been previously uploaded to the Wiki. When you upload several files, they usually end up in different directories (due to the md5 hash on the name), without any way to control it. So, I could easily add a code for defaultDirectory at the beginning of the script (even automatically by the Jmol extension). But my problem is to define this default directory so that it is useful : - there are no files in the root directory for uploads = not a good default directory - the directory where the uploaded file is (uploadedFileContents gives the atom coordinates file) is not the same directory where the surface file is = won't work to find the surface file - ... Nico On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson hans...@stolaf.edu wrote: My point was that if MediaWiki would just insert the Jmol script code for defaultDirectory in the startup script, then the user can include numerous files with no prefix and no concern over where they are. Bob -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
I agree with Nico. The location of uploades files in MW is uncertain. The .jmol file format is in my opinion the way out of this problem: upload a single file with everything included. -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
On 2 Mar 2012, at 13:23, Angel Herráez wrote: I agree with Nico. The location of uploades files in MW is uncertain. The .jmol file format is in my opinion the way out of this problem: upload a single file with everything included. A single file as a zip (the same way that jar files are considered single files). I am however intrigued that the .jvxl file is nowadays a proper XML file, and hence this can itself carry separate namespaces, amounting to different types of content. One can either package eg coordinate and surface files into a single zip archive, or one alternatively could express these components as a single XML file (which can be disentangled into its original components by suitable XML parsing into a DOM). I suppose both alternatives have their advantages and weaknesses. Anyway, Jmol adopts the former approach and this is what we have to find solutions for. -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
oh. never mind then. I thought they went into a specific directory. No, that would not work On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle nverve...@gmail.comwrote: I have the impression that I'm missing a point in this discussion... The situation Henry is talking about is that he need to access several files that have been previously uploaded to the Wiki. When you upload several files, they usually end up in different directories (due to the md5 hash on the name), without any way to control it. So, I could easily add a code for defaultDirectory at the beginning of the script (even automatically by the Jmol extension). But my problem is to define this default directory so that it is useful : - there are no files in the root directory for uploads = not a good default directory - the directory where the uploaded file is (uploadedFileContents gives the atom coordinates file) is not the same directory where the surface file is = won't work to find the surface file - ... Nico On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson hans...@stolaf.edu wrote: My point was that if MediaWiki would just insert the Jmol script code for defaultDirectory in the startup script, then the user can include numerous files with no prefix and no concern over where they are. Bob -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
How does MediaWiki know at all where to look for a file when the script is load xxx.xyz ? On Fri, Mar 2, 2012 at 9:32 AM, Robert Hanson hans...@stolaf.edu wrote: oh. never mind then. I thought they went into a specific directory. No, that would not work On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle nverve...@gmail.comwrote: I have the impression that I'm missing a point in this discussion... The situation Henry is talking about is that he need to access several files that have been previously uploaded to the Wiki. When you upload several files, they usually end up in different directories (due to the md5 hash on the name), without any way to control it. So, I could easily add a code for defaultDirectory at the beginning of the script (even automatically by the Jmol extension). But my problem is to define this default directory so that it is useful : - there are no files in the root directory for uploads = not a good default directory - the directory where the uploaded file is (uploadedFileContents gives the atom coordinates file) is not the same directory where the surface file is = won't work to find the surface file - ... Nico On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson hans...@stolaf.edu wrote: My point was that if MediaWiki would just insert the Jmol script code for defaultDirectory in the startup script, then the user can include numerous files with no prefix and no concern over where they are. Bob -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
Hi Bob, In short, it doesn't know. When you want to display a file that has been previously uploaded, you can use for example jmolFilexxx.xyz/jmolFile. The PHP code of the extension knows where xxx.xyz is stored and creates the script that works. See examples in http://wiki.jmol.org/index.php/MediaWiki/Basic_Example Nico On Fri, Mar 2, 2012 at 4:33 PM, Robert Hanson hans...@stolaf.edu wrote: How does MediaWiki know at all where to look for a file when the script is load xxx.xyz ? On Fri, Mar 2, 2012 at 9:32 AM, Robert Hanson hans...@stolaf.edu wrote: oh. never mind then. I thought they went into a specific directory. No, that would not work On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle nverve...@gmail.comwrote: I have the impression that I'm missing a point in this discussion... The situation Henry is talking about is that he need to access several files that have been previously uploaded to the Wiki. When you upload several files, they usually end up in different directories (due to the md5 hash on the name), without any way to control it. So, I could easily add a code for defaultDirectory at the beginning of the script (even automatically by the Jmol extension). But my problem is to define this default directory so that it is useful : - there are no files in the root directory for uploads = not a good default directory - the directory where the uploaded file is (uploadedFileContents gives the atom coordinates file) is not the same directory where the surface file is = won't work to find the surface file - ... Nico On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson hans...@stolaf.eduwrote: My point was that if MediaWiki would just insert the Jmol script code for defaultDirectory in the startup script, then the user can include numerous files with no prefix and no concern over where they are. Bob -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
How does MediaWiki know at all where to look for a file when the script is load xxx.xyz Probably, the script can NEVER be that. Load is managed with the Jmol MW Extension tags, not with scripts. jmolFile MW knows where to find the wiki file (handled like an image) jmolPdb external jmolSmiles external uploadedFileContents MW knows where to find the wiki file (handled like an image) wikiPageContents MW knows where to find the page inlineContents urlContents external -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
Shouldn't be hard to adapt that to the way Jmol finds file names in scripts: load /*file*/... isosurface /*file*/. next quoted phrase after /*file*/ needs to be replaced by full path to that file. On Fri, Mar 2, 2012 at 9:39 AM, Nicolas Vervelle nverve...@gmail.comwrote: Hi Bob, In short, it doesn't know. When you want to display a file that has been previously uploaded, you can use for example jmolFilexxx.xyz/jmolFile. The PHP code of the extension knows where xxx.xyz is stored and creates the script that works. See examples in http://wiki.jmol.org/index.php/MediaWiki/Basic_Example Nico On Fri, Mar 2, 2012 at 4:33 PM, Robert Hanson hans...@stolaf.edu wrote: How does MediaWiki know at all where to look for a file when the script is load xxx.xyz ? On Fri, Mar 2, 2012 at 9:32 AM, Robert Hanson hans...@stolaf.edu wrote: oh. never mind then. I thought they went into a specific directory. No, that would not work On Fri, Mar 2, 2012 at 7:02 AM, Nicolas Vervelle nverve...@gmail.comwrote: I have the impression that I'm missing a point in this discussion... The situation Henry is talking about is that he need to access several files that have been previously uploaded to the Wiki. When you upload several files, they usually end up in different directories (due to the md5 hash on the name), without any way to control it. So, I could easily add a code for defaultDirectory at the beginning of the script (even automatically by the Jmol extension). But my problem is to define this default directory so that it is useful : - there are no files in the root directory for uploads = not a good default directory - the directory where the uploaded file is (uploadedFileContents gives the atom coordinates file) is not the same directory where the surface file is = won't work to find the surface file - ... Nico On Fri, Mar 2, 2012 at 1:49 PM, Robert Hanson hans...@stolaf.eduwrote: My point was that if MediaWiki would just insert the Jmol script code for defaultDirectory in the startup script, then the user can include numerous files with no prefix and no concern over where they are. Bob -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
no scripts at all? -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
Scripts can be used as you wish, there's just the limitation with paths to files. On Fri, Mar 2, 2012 at 4:46 PM, Robert Hanson hans...@stolaf.edu wrote: no scripts at all? -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
Well, then I propose /*file*/ within a script is adapted by MediaWiki to change that to a proper file name. On Fri, Mar 2, 2012 at 9:51 AM, Nicolas Vervelle nverve...@gmail.comwrote: Scripts can be used as you wish, there's just the limitation with paths to files. On Fri, Mar 2, 2012 at 4:46 PM, Robert Hanson hans...@stolaf.edu wrote: no scripts at all? -- 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces into a Wiki
Henry, maybe loading a .jmol file would help? It can contain the 2 files in it, and the state script. You probably need to allow the new file type to be uploaded to the wiki. -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces into aWiki
On 1 Mar 2012, at 14:24, Jaime Prilusky wrote: On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote: The MediaWiki extension has the following form Overall, this amounts to load isosurface.xyz;isosurface color orange purple isosurface.jvxl translucent; Yes, putting the full filename path does work ( ie images/4/45/isosurface.jvxl ) but part of the reason for creating a Mediawiki extension was to hide such stuff from the user (our users are students, and bright though some of them are, others are bound to find locating the absolute path of a file a tad too much). -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces into aWiki
I think the path is a good lead. If you check the source of the generated wiki page, you should see a path for isosurface.xyz. You probably need to also have the path to isosurface.jvxl, but this is not always obvious which one to use (try Special:FilePath) Nico On Thu, Mar 1, 2012 at 3:24 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote: The MediaWiki extension has the following form Overall, this amounts to load isosurface.xyz;isosurface color orange purple isosurface.jvxl translucent; If your command is isosurface surfile.iso, I understand that you don't need to load the surfile.iso file in advance, but to provide the full path to the file (from the browser point of view), so the isosurface command can access and load the file, and render the content. Jaim -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces into aWiki
Ok, that confirms the explanation. Henry, Yes, the uploadedFileContents tag was designed to hide such complexity from the user (the call to Special:FilePath is done internally by the extension). But using this for scripts would be quite complex because the extension would have to parse the Jmol script... If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. I intend to work again on the extension some time in the future, still not sure when. Nico On Thu, Mar 1, 2012 at 3:45 PM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: On 1 Mar 2012, at 14:24, Jaime Prilusky wrote: On Mar 1, 2012, at 3:35 PM, Rzepa, Henry S wrote: The MediaWiki extension has the following form Overall, this amounts to load isosurface.xyz;isosurface color orange purple isosurface.jvxl translucent; Yes, putting the full filename path does work ( ie images/4/45/isosurface.jvxl ) but part of the reason for creating a Mediawiki extension was to hide such stuff from the user (our users are students, and bright though some of them are, others are bound to find locating the absolute path of a file a tad too much). -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki
On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. If you keep the isosurface file together with the model file, then a simple isosurface tag to indicate the name of the isosurface file (not the full path) can be used to setup the internal default file path to the location of the model file, and call the load. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki
Hi, The extension doesn't manage the path in which files are stored. Depending on the configuration, MediaWiki stores them in several separate folders and there's no way to be sure that 2 files will end up in the same directory. Maybe we can group ideas/suggestions about the syntax for Jmol extension in the talk page of http://wiki.jmol.org/index.php/MediaWiki ? Nico On Thu, Mar 1, 2012 at 4:09 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. If you keep the isosurface file together with the model file, then a simple isosurface tag to indicate the name of the isosurface file (not the full path) can be used to setup the internal default file path to the location of the model file, and call the load. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki
On 1 Mar 2012, at 15:09, Jaime Prilusky wrote: On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. If you keep the isosurface file together with the model file, then a simple isosurface tag to indicate the name of the isosurface file (not the full path) can be used to setup the internal default file path to the location of the model file, and call the load. early versions of .jvxl used to include the coordinates as well as the surface, but (I might have mis-understood) the design nowadays is to keep these as separate files. If of course, it is still possible to write out a .jvxl file with both features, that would solve the immediate problem (but not the general one). -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki
Couldn't you have the uploadedFileContents also set the default directory? In face, one could imagine uploadedFileContents/uploadedFileContents might only set the default directory. On Thu, Mar 1, 2012 at 9:51 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: On 1 Mar 2012, at 15:09, Jaime Prilusky wrote: On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. If you keep the isosurface file together with the model file, then a simple isosurface tag to indicate the name of the isosurface file (not the full path) can be used to setup the internal default file path to the location of the model file, and call the load. early versions of .jvxl used to include the coordinates as well as the surface, but (I might have mis-understood) the design nowadays is to keep these as separate files. If of course, it is still possible to write out a .jvxl file with both features, that would solve the immediate problem (but not the general one). -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki
The problem is that, depending on MediaWiki configuration, uploaded files can end up in different directories (to avoid putting thousands of files in the same directory)... And the user has absolutely no control over which directory will be used for a file. So there's not really a possible default directory... For example, on Jmol wiki, 1ALE.pdb is in images/e/e3 directory, while 1HPNmod.pdb is in images/4/49 Nico On Thu, Mar 1, 2012 at 5:15 PM, Robert Hanson hans...@stolaf.edu wrote: Couldn't you have the uploadedFileContents also set the default directory? In face, one could imagine uploadedFileContents/uploadedFileContents might only set the default directory. On Thu, Mar 1, 2012 at 9:51 AM, Rzepa, Henry S h.rz...@imperial.ac.ukwrote: On 1 Mar 2012, at 15:09, Jaime Prilusky wrote: On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. If you keep the isosurface file together with the model file, then a simple isosurface tag to indicate the name of the isosurface file (not the full path) can be used to setup the internal default file path to the location of the model file, and call the load. early versions of .jvxl used to include the coordinates as well as the surface, but (I might have mis-understood) the design nowadays is to keep these as separate files. If of course, it is still possible to write out a .jvxl file with both features, that would solve the immediate problem (but not the general one). -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
On Mar 1, 2012, at 6:21 PM, Nicolas Vervelle wrote: The problem is that, depending on MediaWiki configuration, uploaded files can end up in different directories (to avoid putting thousands of files in the same directory)... And the user has absolutely no control over which directory will be used for a file. So there's not really a possible default directory... For example, on Jmol wiki, 1ALE.pdb is in images/e/e3 directory, while 1HPNmod.pdb is in images/4/49 Nico Nico, The subdirectories under images/ are computed from the md5 of the file name. $name = 1ALE.pdb; $md5= md5(ucfirst($name)); $fullPath = images/ . substr($md5,0,1) . / . substr($md5,0,2) . / . ucfirst($name); Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
Hi Henry I am senidng to you off-list a sample file I just created. That is a .jmol file (really a zipfile, with contents added by Jmol; I'm not sure if you can collate it manually). This is the procedure I followed: 1. Load the molecule into Jmol app (I used 12.2.16) 2. Create the isosurface, color it etc. 3. Save the isosurface to disk 4. Zap 5. Load the molecule (load command or drag-and-drop) 6. Load the isosurface (isosurface command, drag-and-drop seems to work too) 7. Save all as .JMOL file (I did it from the popup menu) The .jmol file generated this way include both the model and the JVXL files, plus extra niceties like a png, the state script and a manifest). I moved it to a different folder and it loads into Jmol with everything. Note that if you skip step #6 and try to save with the isosurface just created, the file contains the command to generate it but not the isosurface data (as the state script included is recreating the history) So you must load the isosurface from disk. So I bet this is the safest and easiest way to go for the wiki. Good luck! -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
On Thu, Mar 1, 2012 at 6:02 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: On Mar 1, 2012, at 6:21 PM, Nicolas Vervelle wrote: The problem is that, depending on MediaWiki configuration, uploaded files can end up in different directories (to avoid putting thousands of files in the same directory)... And the user has absolutely no control over which directory will be used for a file. So there's not really a possible default directory... For example, on Jmol wiki, 1ALE.pdb is in images/e/e3 directory, while 1HPNmod.pdb is in images/4/49 Nico Nico, The subdirectories under images/ are computed from the md5 of the file name. $name = 1ALE.pdb; $md5= md5(ucfirst($name)); $fullPath = images/ . substr($md5,0,1) . / . substr($md5,0,2) . / . ucfirst($name); Jaim Thanks for the information, But, that still means there's no directory that can be set as default directory for Jmol. And the organization of the files depends also on the wiki configuration (with or without md5 hash, number of characters of the md5 taken into account) and uploads can be mixed between local and shared repository. So having to analyze the script to change file paths is really complex... Nico -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin
Nico, I got the same in the source: /scriptscript src=/mediawiki/extensions/Jmol/Jmol.js?version=3.3_dev_1/scriptscript src=/mediawiki/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1/script/headbody http://132.180.50.97/mediawiki/extensions/Jmol/Jmol.js is not accessible - but I would have expected this, as Jaime suggested to try the COPYRIGHT.txt, and i could not access this one as well. Best Kilian On 30 November 2011 14:10, Nicolas Vervelle nverve...@gmail.com wrote: Ok, So it seems that the extension is active (tags are correctly replaced), but the Jmol part doesn't work at all :( In one of your previous mail, you put a part of the source code of the page for the jmol tag. Can you also send the part that contains the links to the Jmol .js files, that is the head part ? For example on Jmol wiki, I have this : script src=/extensions/Jmol/Jmol.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/Jmol.js?version=3.3_dev_1 /scriptscript src= /extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1 /script Is it correct also on your wiki ? It should be something like /mediawiki/Jmol/Jmol.js for you. Can you access the Jmol.js and JmolMediaWiki.js file through your web server ? The URL http://IP/mediawiki/extensions/Jmol/Jmol.js should be accessible. Nico On Tue, Nov 29, 2011 at 1:38 PM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Hi Nico, I have also tried less complex tags like jmolPdb1ALE/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 -- 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
Re: [Jmol-users] MediaWiki Plugin
Kilian, Please check access rights to the files. It's clear that you can access Jmol.php and Jmol_body.php, since they're are doing their job. In the same directory you must have the COPYRIGHT.txt file and several others. Unless your browser has access to those files, the applet will not appear. Please be sure that files inside extensions/Jmol have permissions 0644 and not more. Some http servers don't like files world writable. Jaim From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 1 Dec 2011 09:45:22 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] MediaWiki Plugin Nico, I got the same in the source: /scriptscript src=/mediawiki/extensions/Jmol/Jmol.js?version=3.3_dev_1/scriptscript src=/mediawiki/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1/script/headbody http://132.180.50.97/mediawiki/extensions/Jmol/Jmol.js is not accessible - but I would have expected this, as Jaime suggested to try the COPYRIGHT.txt, and i could not access this one as well. Best Kilian On 30 November 2011 14:10, Nicolas Vervelle nverve...@gmail.commailto:nverve...@gmail.com wrote: Ok, So it seems that the extension is active (tags are correctly replaced), but the Jmol part doesn't work at all :( In one of your previous mail, you put a part of the source code of the page for the jmol tag. Can you also send the part that contains the links to the Jmol .js files, that is the head part ? For example on Jmol wiki, I have this : script src=/extensions/Jmol/Jmol.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/Jmol.js?version=3.3_dev_1/scriptscript src=/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1/script Is it correct also on your wiki ? It should be something like /mediawiki/Jmol/Jmol.js for you. Can you access the Jmol.js and JmolMediaWiki.js file through your web server ? The URL http://IP/mediawiki/extensions/Jmol/Jmol.js should be accessible. Nico On Tue, Nov 29, 2011 at 1:38 PM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de wrote: Hi Nico, I have also tried less complex tags like jmolPdb1ALE/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.commailto: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 -- 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.netmailto: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.demailto: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.netmailto: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
Re: [Jmol-users] MediaWiki Plugin
Kilian, I think you have a problem in your MW setup, because the file Jmol.js must be accessible. For example, on Jmol wiki, http://wiki.jmol.org/extensions/Jmol/Jmol.js works. It must be accessible otherwise, the HTML page can't retrieve the Javascript functions that are necessary for Jmol. On which OS is your MW ? Have you checked that path name is correctly spelled, including capitalization ? Nico On Thu, Dec 1, 2011 at 9:45 AM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Nico, I got the same in the source: /scriptscript src=/mediawiki/extensions/Jmol/Jmol.js?version=3.3_dev_1/scriptscript src=/mediawiki/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1/script/headbody http://132.180.50.97/mediawiki/extensions/Jmol/Jmol.js is not accessible - but I would have expected this, as Jaime suggested to try the COPYRIGHT.txt, and i could not access this one as well. Best Kilian On 30 November 2011 14:10, Nicolas Vervelle nverve...@gmail.com wrote: Ok, So it seems that the extension is active (tags are correctly replaced), but the Jmol part doesn't work at all :( In one of your previous mail, you put a part of the source code of the page for the jmol tag. Can you also send the part that contains the links to the Jmol .js files, that is the head part ? For example on Jmol wiki, I have this : script src=/extensions/Jmol/Jmol.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/Jmol.js?version=3.3_dev_1 /scriptscript src= /extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1 /script Is it correct also on your wiki ? It should be something like /mediawiki/Jmol/Jmol.js for you. Can you access the Jmol.js and JmolMediaWiki.js file through your web server ? The URL http://IP/mediawiki/extensions/Jmol/Jmol.js should be accessible. Nico On Tue, Nov 29, 2011 at 1:38 PM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Hi Nico, I have also tried less complex tags like jmolPdb1ALE/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 -- 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
Re: [Jmol-users] MediaWiki Plugin
Hi, I really dont get it... a normal page on the wiki looks like http:// IP/mediawiki/index.php/Special:Version and in the source, there is /scriptscript src=/mediawiki/extensions/ Jmol/Jmol.js?version=3.3_dev_1 so i assume, it should be possible to access Jmo.js via http:// IP/mediawiki/extensions/Jmol/Jmol.js But i simply cant I tried for another extension, its the same problem. Example Is UserMerge, which can be used exactly as it should but i cannot access http:// IP/mediawiki/extensions/UserMerge/UserMerge.php. I will have to look into this Kilian -- 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
Re: [Jmol-users] MediaWiki Plugin
Killian, On your test, try always to access a plain text, html or image file (.txt, .html, .png, .gif) Files ending on .php will get a different treatment on the server side and many times you will be unable to see them from a browser. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel jaime.prilu...@weizmann.ac.ilmailto: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.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 1 Dec 2011 11:02:21 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] MediaWiki Plugin Hi, I really dont get it... a normal page on the wiki looks like http://IP/mediawiki/index.php/Special:Version and in the source, there is /scriptscript src=/mediawiki/extensions/Jmol/Jmol.js?version=3.3_dev_1 so i assume, it should be possible to access Jmo.js via http://IP/mediawiki/extensions/Jmol/Jmol.js But i simply cant I tried for another extension, its the same problem. Example Is UserMerge, which can be used exactly as it should but i cannot access http://IP/mediawiki/extensions/UserMerge/UserMerge.php. I will have to look into this Kilian -- 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.netmailto: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
Re: [Jmol-users] MediaWiki Plugin
Jaim, its exactly the same. This is what i get: Not Found The requested URL /mediawiki/extensions/UserMerge/blubb.txt was not found on this server. - same as for jmol files. Btw, rights are set as you told me (as for all other extensions). Kilian -- 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
Re: [Jmol-users] MediaWiki Plugin
Kilian, The problem may be due to your web server configuration then (accessing of text file is only done through web server not MW software). What is your web server ? (Apache HTTPD, ...) What version ? On which OS ? What is the content of your configuration files ? Can you try putting the .txt file at different levels in the directory hierarchy and see if it works at some levels ? Nico On Thu, Dec 1, 2011 at 12:09 PM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Jaim, its exactly the same. This is what i get: Not Found The requested URL /mediawiki/extensions/UserMerge/blubb.txt was not found on this server. - same as for jmol files. Btw, rights are set as you told me (as for all other extensions). Kilian -- 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
Re: [Jmol-users] MediaWiki Plugin
Strange. Can you retrieve http://YOUR_IP/mediawiki/README and http://YOUR_IP/mediawiki/extensions/README ? Those files are part of a default MediaWiki installation and should be there. If you're running on linux, it could be a SELinux problem. Try to disable temporarily SELinux echo 0 /selinux/enforce And after testing Jmol, you can enable it again with echo 1 /selinux/enforce Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel jaime.prilu...@weizmann.ac.ilmailto: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.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 1 Dec 2011 12:09:54 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] MediaWiki Plugin Jaim, its exactly the same. This is what i get: Not Found The requested URL /mediawiki/extensions/UserMerge/blubb.txt was not found on this server. - same as for jmol files. Btw, rights are set as you told me (as for all other extensions). Kilian -- 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.netmailto: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
Re: [Jmol-users] MediaWiki Plugin
Nico, sorry for double posting. The OS is Ubuntu Server. And I cannot access the INSTALL file of the mediawiki itself, which is perfectly possible on the jmol wiki. There is something quite wrong here.,.. Best Kilian -- 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
Re: [Jmol-users] MediaWiki Plugin
Hi, Oh man I think i got it... Mediawiki on Ubuntu is split over three directories: /etc/mediawiki and /etc/mediawiki-extensions, /usr/share/mediawiki and /usr/share/mediawiki-extensions, /usr/share/mediawiki and /usr/share/mediawiki-extensions and /var/lib/mediawiki. Files are only directly accessibleis present or linked to the folders residing in var/lib. I linked the Jmol extension into /var/lib/mediawiki from /usr/share/mediawiki-extensions. Now it seems to work, at least the applet displays a molecule... So sorry for stealing you time that long. I really appreciate all your help. Best Kilian On 1 December 2011 12:43, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Nico, sorry for double posting. The OS is Ubuntu Server. And I cannot access the INSTALL file of the mediawiki itself, which is perfectly possible on the jmol wiki. There is something quite wrong here.,.. Best Kilian -- __ 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
Re: [Jmol-users] MediaWiki Plugin
No problem, Enjoy playing with the extension. I hope to be able to work on it again soon. Nico On Thu, Dec 1, 2011 at 1:05 PM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Hi, Oh man I think i got it... Mediawiki on Ubuntu is split over three directories: /etc/mediawiki and /etc/mediawiki-extensions, /usr/share/mediawiki and /usr/share/mediawiki-extensions, /usr/share/mediawiki and /usr/share/mediawiki-extensions and /var/lib/mediawiki. Files are only directly accessibleis present or linked to the folders residing in var/lib. I linked the Jmol extension into /var/lib/mediawiki from /usr/share/mediawiki-extensions. Now it seems to work, at least the applet displays a molecule... So sorry for stealing you time that long. I really appreciate all your help. Best Kilian On 1 December 2011 12:43, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Nico, sorry for double posting. The OS is Ubuntu Server. And I cannot access the INSTALL file of the mediawiki itself, which is perfectly possible on the jmol wiki. There is something quite wrong here.,.. Best Kilian -- __ 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
Re: [Jmol-users] MediaWiki Plugin
Hi Nico,
I have also tried less complex tags like jmolPdb1ALE/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://x/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
RD 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
size150/size
inlineContents
REMARK Butane
HETATM1 C UNK 0 -0.769 0.000 0.000 C
HETATM2 C UNK 0 0.769 0.000 0.000 C
HETATM3 C UNK 0 -1.383 -0.728 1.203 C
HETATM4 C UNK 0 1.382 -0.741 1.196 C
HETATM5 H UNK 0 -1.127 1.059 0.007 H
HETATM6 H UNK 0 -1.142 -0.461 -0.945 H
HETATM7 H UNK 0 -1.001 -0.311 2.163 H
HETATM8 H UNK 0 1.128 -0.488 -0.940 H
HETATM9 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
jmolFileMIL53_mimik_Loiseau.xyz/jmolFile
The source code of the page then shows this section, which I take
for the jmol part:
pa 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
pbr!-- Jmol --script type=text/javascript
//![CDATA
Re: [Jmol-users] MediaWiki Plugin
Ok, So it seems that the extension is active (tags are correctly replaced), but the Jmol part doesn't work at all :( In one of your previous mail, you put a part of the source code of the page for the jmol tag. Can you also send the part that contains the links to the Jmol .js files, that is the head part ? For example on Jmol wiki, I have this : script src=/extensions/Jmol/Jmol.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/Jmol.js?version=3.3_dev_1 /scriptscript src=/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1 /script Is it correct also on your wiki ? It should be something like /mediawiki/Jmol/Jmol.js for you. Can you access the Jmol.js and JmolMediaWiki.js file through your web server ? The URL http://IP/mediawiki/extensions/Jmol/Jmol.js should be accessible. Nico On Tue, Nov 29, 2011 at 1:38 PM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.de wrote: Hi Nico, I have also tried less complex tags like jmolPdb1ALE/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 -- 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
Re: [Jmol-users] MediaWiki Plugin
On line 833 of the file Jmol.body.php remove the '' from the third parameter of the function jmolTag() Jaim -- Dr Jaime Prilusky Head Bioinformatics RD 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.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 24 Nov 2011 14:15:24 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: [Jmol-users] MediaWiki Plugin Dear all, I am trying to use Jmol within our Wiki. I have installed the Mediawiki extension according to the documentation, placing both the source files of the extension and the files of Jmol in a Jmol folder within the extensions folder of mediawiki. Having set require_once(extensions/Jmol/Jmol.php); the source code of an applet is no longer displayed, so the parser seems so acknowledge the presence of known tags,but no applet is displayed. Did anyone come across this issue, or does anyone see an obvious mistake of mine? Many thanks for your help Kilian Baerwinkel -- __ 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.demailto: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.netmailto: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
Re: [Jmol-users] MediaWiki Plugin
Hello Jaime Thank you very much for your answer... On line 833, there was no at the third parameter, but i fond some more $parser and removed the . This did not make the applet appear, but now i can see a link if I insert a jmolfile. Still nothing happens if the link is clicked. Any ideas? Best Kilian On 24 November 2011 14:34, Jaime Prilusky jaime.prilu...@weizmann.ac.ilwrote: On line 833 of the file Jmol.body.php remove the '' from the third parameter of the function jmolTag() Jaim -- Dr Jaime Prilusky Head Bioinformatics RD 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 14:15:24 +0100 To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] MediaWiki Plugin Dear all, I am trying to use Jmol within our Wiki. I have installed the Mediawiki extension according to the documentation, placing both the source files of the extension and the files of Jmol in a Jmol folder within the extensions folder of mediawiki. Having set require_once(extensions/Jmol/Jmol.php); the source code of an applet is no longer displayed, so the parser seems so acknowledge the presence of known tags,but no applet is displayed. Did anyone come across this issue, or does anyone see an obvious mistake of mine? Many thanks for your help Kilian Baerwinkel -- __ 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
Re: [Jmol-users] MediaWiki Plugin
Take a look to your web server error log file. Sometimes PHP errors appear there and you may learn something from that. Look to the source of the wiki generated page to see if the structure of the jmolApplet makes sense. Create a really simple page with only an applet, no links nor text and try to make it work. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD 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.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 24 Nov 2011 15:23:43 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] MediaWiki Plugin Hello Jaime Thank you very much for your answer... On line 833, there was no at the third parameter, but i fond some more $parser and removed the . This did not make the applet appear, but now i can see a link if I insert a jmolfile. Still nothing happens if the link is clicked. Any ideas? Best Kilian On 24 November 2011 14:34, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: On line 833 of the file Jmol.body.php remove the '' from the third parameter of the function jmolTag() Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot – Israel mail: jaime.prilu...@weizmann.ac.ilmailto: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.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 24 Nov 2011 14:15:24 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: [Jmol-users] MediaWiki Plugin Dear all, I am trying to use Jmol within our Wiki. I have installed the Mediawiki extension according to the documentation, placing both the source files of the extension and the files of Jmol in a Jmol folder within the extensions folder of mediawiki. Having set require_once(extensions/Jmol/Jmol.php); the source code of an applet is no longer displayed, so the parser seems so acknowledge the presence of known tags,but no applet is displayed. Did anyone come across this issue, or does anyone see an obvious mistake of mine? Many thanks for your help Kilian Baerwinkel -- __ MSc. Chem. Kilian Bärwinkel Lehrstuhl für Anorganische Chemie I Fakultät NW 1 Universität Bayreuth Universitätsstr. 30 95447 Bayreuth Tel:+49 921 55 - 4387tel:%2B49%20921%2055%20-%204387 Fax:+49 921 55 - 2788tel:%2B49%20921%2055%20-%202788 e-mail: kilian.baerwin...@uni-bayreuth.demailto: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.netmailto:Jmol-users@lists.sourceforge.nethttps://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.netmailto: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.demailto: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
Re: [Jmol-users] MediaWiki Plugin
Hello Kilian First, to be sure, please confirm that you are using the Jmol Mediawiki Extension and what version it is. Also, version of MediaWiki may be of relevance. You mention a jmolfile tag but that is not included in v.3.3 which is the one documented at the Jmol Wiki. So I guess you are using the newer version at mediawiki.org (I'm not familiar with that one) We are a bit behind on documentation, I see :-( -- 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
Re: [Jmol-users] MediaWiki Plugin
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
Re: [Jmol-users] MediaWiki Plugin
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 RD 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
