Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces into a Wiki

2012-03-01 Thread Angel Herráez
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces into aWiki

2012-03-01 Thread Rzepa, Henry S
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces into aWiki

2012-03-01 Thread Nicolas Vervelle
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,

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces into aWiki

2012-03-01 Thread Nicolas Vervelle
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki

2012-03-01 Thread Jaime Prilusky
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki

2012-03-01 Thread Nicolas Vervelle
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki

2012-03-01 Thread Rzepa, Henry S
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki

2012-03-01 Thread Robert Hanson
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki

2012-03-01 Thread Nicolas Vervelle
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki

2012-03-01 Thread Jaime Prilusky
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki

2012-03-01 Thread Angel Herráez
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

Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki

2012-03-01 Thread Nicolas Vervelle
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