RE: [Jmol-users] beginning Jmol website
If you have the file somewhere else (say above the Jmol file), can you just use the complete path (i.e. URL) to the file? Robley Light -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Miguel Sent: Thursday, July 07, 2005 4:18 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] beginning Jmol website I see the file there from my ftp program, so I'm confused. My page is at http://web.centre.edu/muzyka/organic/butane/simple.htm butane.xyz does not exist in the same directory as simple.htm Restated, this file should exist, but does not: http://web.centre.edu/muzyka/organic/butane/butane.xyz If you *really* think that you see it in the same directory, then check the spelling and check the CASE of the filename (although I do not believe that case sensitivity should be an issue since your web server is running Windows). Miguel --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
RE: [Jmol-users] beginning Jmol website
If you have the file somewhere else (say above the Jmol file), can you just use the complete path (i.e. URL) to the file? It is generally best if you use 'relative paths' to reference other files. That way you can restructure your web site more easily. In other words, do not start your references with http://my.server.com/some/path Rather, start your file references with things like ../ # for parent directory subdirectory/ ../siblingDirectory/ Miguel --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
RE: [Jmol-users] beginning Jmol website
Robley and Jennifer, it is not a question of relative or absolute paths, it is that Java will refuse to load files that are above the applet in the folder tree structure, due to security reasons. So, you can have /JmolApplet.jar /molecule.mol or /JmolApplet.jar /models/molecule.mol but not /jmol/JmolApplet.jar /molecule.mol I think jmol.js can be anywhere, although I just put it together with JmolApplet.jar at the root of my website, so that all pages and models can read it. Miguel recommends --as the foolproof way-- putting JmolApplet.jar and the models in the same folder, but that is inconvenient in my website structure, as I like to classify content in separate modules. El 8 Jul 2005 a las 2:59, Robley Light escribió: If you have the file somewhere else (say above the Jmol file), can you just use the complete path (i.e. URL) to the file? --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
RE: [Jmol-users] beginning Jmol website
On 2005-07-08 (12:48) Angel Herraez wrote: Robley and Jennifer, it is not a question of relative or absolute paths, it is that Java will refuse to load files that are above the applet in the folder tree structure, due to security reasons. So, you can have /JmolApplet.jar /molecule.mol or /JmolApplet.jar /models/molecule.mol but not /jmol/JmolApplet.jar /molecule.mol snip just to clarify - the above restriction applies to LOCAL use of an applet only. if you are running from an actual Web server, you can put JmolApplet, Jmol.js, and your pdb files anywhere in relation to each other as long as they are www-readable, and the paths and filenames and permissions are correct. you can even put them on different servers. BTW, one easy way to circumvent the restriction on local dir structure is to use the signed applet instead. regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. http://www.molvisions.com/ usa:north carolina:raleigh Mathematics is the language with which God has written the universe. - Galileo Galilei --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] beginning Jmol website
On 2005-07-08 (13:27) Egon Willighagen wrote: On Friday 08 July 2005 01:17 pm, timothy driscoll wrote: if you are running from an actual Web server, you can put JmolApplet, Jmol.js, and your pdb files anywhere in relation to each other as long as they are www-readable, and the paths and filenames and permissions are correct. you can even put them on different servers. Is that true? Then why aren't people reusing the Jmol.jar from the jmol.org website? That would put it in the cache and considerably reduce download of Jmol-activated pages! It would be sort of plugin then, right? but it would cause a traffic bottleneck, no? I must confess that I have not tested the applet from different servers, so I am not absolutely positive that setup works. I hadn't really thought about serving the applet from a third-party server. I actually meant that you can run Jmol on your server and load pdb files from, say, the RCSB. there was some talk on the list about using Jmol.js from the Jmol site - IIRC, Bob Hanson was doing this at some point (Bob can you comment?). and I have done it in various other contexts. so I don't see why the applet wouldn't work; I just haven't tried. regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. http://www.molvisions.com/ usa:north carolina:raleigh Life is just one damned thing after another. - Elbert Hubbard --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] beginning Jmol website
On 2005-07-08 (13:27) Egon Willighagen wrote: On Friday 08 July 2005 01:17 pm, timothy driscoll wrote: if you are running from an actual Web server, you can put JmolApplet, Jmol.js, and your pdb files anywhere in relation to each other as long as they are www-readable, and the paths and filenames and permissions are correct. you can even put them on different servers. Is that true? Then why aren't people reusing the Jmol.jar from the jmol.org website? That would put it in the cache and considerably reduce download of Jmol-activated pages! It would be sort of plugin then, right? ok, just tested it - running the applet and the html file from different servers does NOT appear to work (Jmol.js alerts that the codebase should be a relative url, not absolute). to be honest, I did not really think about that option when I wrote my response. my apologies for being less than clear in my supposed clarifying comment. :-/ ignore my sentence 'you can even put them on different servers' and the rest is true, though. :-) regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. http://www.molvisions.com/ usa:north carolina:raleigh To give anything less than your best is to sacrifice the gift. - Steve Prefontaine --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] beginning Jmol website
Hi Jennifer I have seen this before. Most likely it is due to jmol applet being in a directory **under** that of the model. This is a known problem, though I thought I understood it was so only for local files, no web server files. Anyway, for a start try putting jmolapplet.jar in the same folder/directory as the model. If that doesn't fix the errors, post again. On 7 Jul 2005 at 14:44, Jennifer L. Muzyka wrote: I'm finally trying to start converting some of my chime tutorials to jmol, and I'm having a tough time getting a very simple example to work. I basically copied the simple example in the demonstration pages. I've tried several approaches, all of them unsuccessful. I tried running the page from my desktop. That doesn't work, but I vaguely remember reading that the page has to be running from a server. So I tried running the page from my server. In both of these cases, the little black jmol box appears but no molecule is loaded. I read the java console and it looks like the molecule isn't getting loaded from my desktop because of some violation. From the server, there's a message that says the file isn't found. I see the file there from my ftp program, so I'm confused. My page is at http://web.centre.edu/muzyka/organic/butane/simple.htm I was reading through the old messages on the archive to see if there's some stupid thing I'm doing wrong. From April 26 (in response to Kevin Parkes' message), I see there's a problem with jmol.js. So I downloaded the latest version of jmol.js from http://www.jmol.org/jmol/Jmol.js and the error messages I get are even scarier. I also tried a demo referred to in that same thread ( http://www.jmol.org/demo/jssample3) and I get messages similar to the ones I saw when I used that version of the Jmol.js. I'm thinking the version of Jmol.js I downloaded (dated May 14, 2005) might have a problem. But whatever I did previously wasn't working either. I would appreciate any advice that anybody can offer. -Jennifer --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] beginning Jmol website
I see the file there from my ftp program, so I'm confused. My page is at http://web.centre.edu/muzyka/organic/butane/simple.htm butane.xyz does not exist in the same directory as simple.htm Restated, this file should exist, but does not: http://web.centre.edu/muzyka/organic/butane/butane.xyz If you *really* think that you see it in the same directory, then check the spelling and check the CASE of the filename (although I do not believe that case sensitivity should be an issue since your web server is running Windows). Miguel --- This SF.Net email is sponsored by the 'Do More With Dual!' webinar happening July 14 at 8am PDT/11am EDT. We invite you to explore the latest in dual core and dual graphics technology at this free one hour event hosted by HP, AMD, and NVIDIA. To register visit http://www.hp.com/go/dualwebinar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
