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
