Re: [Jmol-users] possible problem with older scripts
This page works fine on my Windows machine (XP Sp3, with IE 7). Robley Light * Robley J. Light Professor Emeritus of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: [EMAIL PROTECTED] 95 Chieftan Way Fax: (850) 644-8281 Florida State UniversityHome Page: http://www.chem.fsu.edu/editors/rlight Tallahassee, FL 32306-4390 -Original Message- From: William Reusch [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 29, 2008 3:17 PM To: sourceforge Subject: [Jmol-users] possible problem with older scripts Hi, I am impressed by the advancements that Bob and others have made over the past year, but my reluctance to change what is working has deferred my examination of newer versions of Jmol. I now find that scripts that are working well with an early 2007 version of Jmol seem to have a liveconnect problem in version 11.6.1, in that buttons that change the atom display or load a new molecule no longer work. This test consisted of placing a copy of a functioning html file in the jmol-11.6.1 folder downloaded from sourceforge, along with necessary pdb files, and running it from a freshly booted system. Admittedly, this script does not use the recommended javascript library, but I prefer to script the applet directly, and I fear my time investment in existing scripts will prohibit me from upgrading. The platform is a Mac G4 running OS 10.3.9. The browsers are Firefox and Safari. I will test this on a Windows machine later. This simple example is: http://www.cem.msu.edu/~reusch/VirtTxtJml/demo.htm http://www.cem.msu.edu/%7Ereusch/VirtTxtJml/demo.htm Bill -- --- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] polyhedra files
Several weeks ago I asked the list if anyone knew of files that could display geometric shapes (for a lower grade math and science project). I'd like to thank Bob Hanson and Dean Johnston who not only put me on to a source of the xyz files but explained how to use Jmol.js to draw the edges and faces. In case anyone else is interested, I've posted these structures at http://chemweb.chem.fsu.edu/editors/rlight/polyhedra/index.html Feel free to use them. You can modify the spt files if you want to change the face colors. I've also written a problem in LON-CAPA using them (published publicly so it isn't necessary to log in to a LON-CAPA server or course to see it). http://loncapa10.fsu.edu/res/fsu/rlight/GEO/Polyhedra.problem Robley Light * Robley J. Light Professor Emeritus of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: [EMAIL PROTECTED] 95 Chieftan Way Fax: (850) 644-8281 Florida State UniversityHome Page: http://www.chem.fsu.edu/editors/rlight Tallahassee, FL 32306-4390 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Are there any files available displaying simple geometric solids
Its been a while since I've monitored this list, so forgive me if this is a question that has been asked and answered in the past. I'm working on a project related to some lower-grade math and science and I would like to use Jmol to display a variety of 3D solids (the five platonic ones, perhaps plus some other irregular ones). I can use ChemDraw to make a cube and tetrahedron of carbon atoms, save as a mol file, bring into Chem3D, delete the hydrogens, and minimize--producing a passable mol or pdb file for a cube and a tetrahedron. I can probably spend some time trying to figure out the coordinate values to make the bonds longer, and I understand I can use Jmol.js commands to work on how to display these structures (still trying to learn that). Before trying to do this with more complex shapes, though, does anyone know of a repository of such geometric files that have already been created? (I've spent a couple of hours with Google with out success). Or, does anyone have a suggestion of how to do this more easily (and elegantly)? Thanks. Robley Light * Robley J. Light Professor Emeritus of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: [EMAIL PROTECTED] 95 Chieftan Way Fax: (850) 644-8281 Florida State UniversityHome Page: http://www.chem.fsu.edu/editors/rlight Tallahassee, FL 32306-4390 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How long to load Jmol?
See last set below (first name Robley) IE7 on Windows XP * Robley J. Light Professor Emeritus, Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: [EMAIL PROTECTED] Florida State UniversityFax: (850) 644-8281 Tallahassee, FL 32306-4390Home Page: http://www.chem.fsu.edu/editors/rlight -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bob Hanson Sent: Friday, April 27, 2007 11:51 PM To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] How long to load Jmol? I need some help sorting out a couple of things. One thing we need to do is separate the load time for Jmol from the load time of Java. So: first, open your browser so we aren't testing browser opening times. Then please go here to load Java at http://java.sun.com/applets/jdk/1.3/demo/applets/Clock/example1.html Then, while looking at your watch, click each of the links below and report back how many seconds it takes before you see the molecule. (I guess I could have put a timer in there, but I didn't.) You get one shot at this -- doesn't count the second time you click. The first letter of your first name determines which order to click: If your first name begins with A-F, click in this order: http://www.stolaf.edu/people/hansonr/jmol/pi/simplejar.htm http://www.stolaf.edu/academics/chemapps/jmol/temp/class/simplejar.htm http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11 /simplejar.htm If G -O, click in this order: http://www.stolaf.edu/academics/chemapps/jmol/temp/class/simplejar.htm http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11 /simplejar.htm http://www.stolaf.edu/people/hansonr/jmol/pi/simplejar.htm If N-Z, click this order: http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11 /simplejar.htm 20 seconds http://www.stolaf.edu/academics/chemapps/jmol/temp/class/simplejar.htm Didn't catch exactly--between 15 and 20 http://www.stolaf.edu/people/hansonr/jmol/pi/simplejar.htm 18 seconds Thanks, Bob I've cleared my cache, closed my browser, and done everything I can to slow this down, and from here (home, different net), it seems to load nearly instantly. So I suspect I really haven't cleared this out completely. Thanks, Bob -- --- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
RE: [Jmol-users] sound (noise)
Or a_cellular_phone? * Robley J. Light Professor of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: [EMAIL PROTECTED] Florida State University Fax: (850) 644-8281 Tallahassee, FL 32306-4390Home Page: http://www.chem.fsu.edu/editors/rlight -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Phillip Barak Sent: Wednesday, December 14, 2005 2:37 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] sound (noise) I have produced Chime animations with integrated audio, so technologically, it can be done. now how you would 'record' the noise of a molecular vibration... you got me. a really tiny ear? How about a _micro_phone? --Phil --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
RE: [Jmol-users] Loop Command in Chime
Nice script and presentation. It loops for me with Firefox 1.0.7 and Netscape 8.0, but shows funny behaviour in IE 6. I get an error message when the loop command comes around and the animation stops. Clicking refresh does not reload the script from the beginning but just loads a stationary top view of the helix. This is on a Windows XP machine. You might want to try posting the question at molvis-list, run by Eric Martz and Tim Driscoll, (though Tim reads this list). https://bioinformatics.org/mailman/listinfo/molvis-list Robley Light * Robley J. Light Professor of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: [EMAIL PROTECTED] Florida State University Fax: (850) 644-8281 Tallahassee, FL 32306-4390Home Page: http://www.chem.fsu.edu/editors/rlight -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of John Tweedie Sent: Tuesday, November 01, 2005 4:37 PM To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] Loop Command in Chime Hello I don't know if this is the right mailing list to use for RasMol/Chime questions. If not please excuse. Has anyone had a problem with the Chime loop command when using Internet Explorer on a PC? Our local Science Centre has asked me to prepare a display for an exhibit on the history of the discovery of the DNA structure. I have made a script with a loop command that works fine on my Mac (A G4 iMac running Classic mode in 10.3.9 with Netscape Communicator 4.78. I am at a bit of a loss. I have been experimenting a bit with jmol but I am not into javascript and for most of what I do Rasmol and Chime are fine. You can look at the display at http://imbs.massey.ac.nz/DNA_Loop/DNA_Loop.htm Cheers John Tweedie Associate Professor in Biochemistry Institute of Molecular BioSciences Te Kura Putaiao Koiora-a-Ngota College of Sciences Massey University Private Bag 11 222 Palmerston North New Zealand Phone:(64)(6) 350 5515 Extension 2581 Fax: (64)(6) 350 5688 [EMAIL PROTECTED] --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42 plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ 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? 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
