[Jmol-users] Implementation of antialiasing in Jmol
Hi, I'm interested in the implementation of the antialiasing in Jmol, and I guess whether there are any (undocumented ?) options for controlling the quality. The quality is good, but would be interesting to try the highest quality if there were options. It could be say 2x2 supersampling, ie. render to a framebuffer twice the dimensions of the applet window and reduce down with simple averaging of 4 pixels into 1. Simple but consumes frame buffer space and costs 4x polygon fill load. Or it could be MultiSample rendering into a dithered grid of subpixel locations, in which case you can have 2, 4, 6, 8 or other numbers of sample points, and there are many choices of the grid of subpixel locations. http://en.wikipedia.org/wiki/Supersample_anti-aliasing http://en.wikipedia.org/wiki/Multisample_anti-aliasing I have an academic/historic interest in this, I worked for SGI for 15 years, during which they introduced the Reality Engine and later models with hardware multisample antialising, and we spent much time working with it, measuring quality and performance in detail. It's all pretty standard now in Nvidia and ATI graphics cards. I'm pretty rusty on the latest developments, apologies if the above is inaccurate. I couldn't find anything detailed in the Jmol mailing list archives. Thanks, Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] (no subject)
Ciao Pino http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Functions_that_s et_CSS_rules explains it. I found jmol.setAppletCss. Where should I insert the script and what can be the exat sintax? Not exact, but something like this: Before the call to getJmolApplet: Jmol.setAppletCss(.toLeft) as long as you have defined the css code for class toLeft or Jmol.setAppletCss(style='float:left') -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with Jmol export to web?
Maybe we should make this patch to the templates as a temporary fix. I agree with that. If it is confirmed that current Java policies block local file loading, just change the code to force the signed applet. It is important to keep E2W useful. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jsmol: Problem downloading png/jmol
Hello, i use jsmol on my website. Everthing works fine but i cannot download the view anymore (as png or jsmol). I changed nothing. I got the following error message: Not Found The requested URL /jmol/jsmol/jsmol.php was not found on this server. Apache Server at chemapps.stolaf.edu Port 80 Can sombody help me? Best thanks Björn Gohlke -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] R: Re: (no subject)
Thanks Angel. I will try it again as soon as possible. I saw already that page and the function and i tried to put into the script containing jmol:applet. Nothing working... i will try it again. maybe the sintax was wrong. If i am right i need to put the jmol.setAppletCss before the jmolApplet0. Pino Messaggio originale Da: angel.herr...@uah.es Data: 17/09/2013 9.42 A: pino.stricc...@libero.itpino.stricc...@libero.it, jmol-users@lists. sourceforge.net Ogg: Re: [Jmol-users] (no subject) Ciao Pino http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Functions_that_s et_CSS_rules explains it. I found jmol.setAppletCss. Where should I insert the script and what can be the exat sintax? Not exact, but something like this: Before the call to getJmolApplet: Jmol.setAppletCss(.toLeft) as long as you have defined the css code for class toLeft or Jmol.setAppletCss(style='float:left') -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jsmol: Problem downloading png/jmol
Add php to the file location. Change the path to /jmol/jsmol/php/jsmol.php Jaim On Sep 17, 2013, at 1:57 PM, björn bjoern-oliver.goh...@charite.de wrote: Hello, i use jsmol on my website. Everthing works fine but i cannot download the view anymore (as png or jsmol). I changed nothing. I got the following error message: Not Found The requested URL /jmol/jsmol/jsmol.php was not found on this server. Apache Server at chemapps.stolaf.edu Port 80 Can sombody help me? Best thanks Björn Gohlke -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] resizable JSmol image is distorted on resize
Hi all This is an older problem that was solved and it seems now to be back in JSmol which I downloaded yesterday (jmol-13.3.6_2013.09.14.zip from StOlaf) In the HTML5 mode, when the container is resized (I'm using jQuery resizable for that and 100% Jmol Object), the model image gets distorted until you go and drag the model around again. I'm quite sure this was fixed time ago. I may have a mixture of jQuery versions (my external one and that included by JSmol, but I've been unable to use JSmol.nojq.min.js) but I dont think it should be that since everything else is working fine. Any inspiration, Bob? If you don't have one, I will try to set up test pages -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jsmol -- local file reading/drag drop and local file writing
Bob, I have a biochemist friend doing some testing of the local read/write. It works on my Mac Safari for small molecules. On the write dialog box, is there any way to trap a cancel button before the cancel result hits the server PHP? As it is, a cancel simply generates a PHP error that's automatically saved on Mac/Safari. This will be a bit confusing to users. I'm still trying to save individual model rotation and conformation rotation on a keyless iPad. I'm stumped. Now that unbind LEFT cuts subsequent drag script binding off also, binding LEFT to a new script will not work for drag related scripts. I can sill bind LEFT to other scripts as long as they do not involve drag. After the unbind LEFT however, the screen is dead to any scripts involving dragging. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Sep 16, 2013, at 6:54 PM, Robert Hanson wrote: OK. I have uploaded changes to Jmol that allow JSmol/HTML5 to read and write files to a local drive. Whew! That was tricky -- text, binary, zip, gzip, pngj, xml -- I checked as many as I could find. Please test on a variety of platforms: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.16.zip top center column -- local file read write Bob ___JmolVersion=13.3.6_dev_2013.09.16 bug fix: chains improperly selected in JSmol/HTML5 bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local drive. bug fix: JSmol/HTML5 not allowing WRITE FILE ? bug fix: platformSpeed persists but appears unreadable after loading a state bug fix: JavaScript version InputStreamReader not processing non-UTF data correctly bug fix: second reading of older PNG files with embedded script fails due to improper png file caching new feature: set drawFontSize // defaults to 14.0 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Problem with Jmol export to web?
After testing a sample from Art this is my diagnosis: Nothing to do with Jmol version or broken E2W. It's the Java security blocking the applets from local disk. I've had this problem for months now and haven't found any solution other than uploading to a web server or running a local webserver. (Firefox, Win7 or Win8) -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] error in loading the applet in JSmol
Hi Friends, while doing some trials with formatting to float left the applet in JSmol i run into this error when starting the JSmol. Jmol._Canvas2D (JSmol) jmolApplet0[x] call loadScript core\package.js call loadScript core\package.js -- required by w3c script failed What has Happened? Pino -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 13.[2/3].6 reading/writing - how cool is this?
Used to be that it required the signed applet to read and write files locally. Well, well, what do you know? I'm liking HTML5 more and more. The following commands, previously for the signed applet only, now work in JSmol/HTML5. load ? x = load(?) write file ? write xxx.jpg write xxx.png write PNGJ xxx.png write PNGJ 500 500 xxx.png write xxx.zip write xxx.jmol write xxx.pdbwrite xxx.mol write xxx.v2000 write xxx.v3000 write xxx.xyz What's especially satisfying for me is that the loading is done asynchronously. I had thought that would be extremely difficult to do -- to pause a running script of however many levels of depth and deep into however many function calls while an asynchronous file load was happening, then restart upon completion at the right place. Well, guess what? It was only moderately difficult! The HTML5 FileReader API is great. [ http://www.w3.org/TR/FileAPI/ ] Looks like this has reasonable support across browsers (http://caniuse.com/#feat=filereader), although one cannot go back very far in time. Writing files to disk still requires reflecting the data from Info.serverUrl, but I'm optimistic (based on http://caniuse.com/filesystem) that the HTML5 FileWriter API will continue to be introduced and at some point will allow us to get rid of the need of a server for local file writing. Certainly what we have now is close to ideal. Check it out at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.17.zip Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.[2/3].6 reading/writing - how cool is this?
Bob, The writing and loading file features that you just introduced in JSmol are truly innovative and take JSmol to a new level. Excellent job. However, I do have one aesthetic suggestion: When loading files into JSmol from a local machine, a new panel with BROWSE/LOAD/CANCEL buttons appears on the page and a prompt window only appears after clicking on the BROWSE button. Is it possible to go straight to the prompt window (as happens with Jmol when loading a file) to select a file of your choice in lieu of having to go through the BROWSE button? Just some thoughts. Thanks! Amjad On Tue, Sep 17, 2013 at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: Used to be that it required the signed applet to read and write files locally. Well, well, what do you know? I'm liking HTML5 more and more. The following commands, previously for the signed applet only, now work in JSmol/HTML5. load ? x = load(?) write file ? write xxx.jpg write xxx.png write PNGJ xxx.png write PNGJ 500 500 xxx.png write xxx.zip write xxx.jmol write xxx.pdbwrite xxx.mol write xxx.v2000 write xxx.v3000 write xxx.xyz What's especially satisfying for me is that the loading is done asynchronously. I had thought that would be extremely difficult to do -- to pause a running script of however many levels of depth and deep into however many function calls while an asynchronous file load was happening, then restart upon completion at the right place. Well, guess what? It was only moderately difficult! The HTML5 FileReader API is great. [ http://www.w3.org/TR/FileAPI/ ] Looks like this has reasonable support across browsers (http://caniuse.com/#feat=filereader), although one cannot go back very far in time. Writing files to disk still requires reflecting the data from Info.serverUrl, but I'm optimistic (based on http://caniuse.com/filesystem) that the HTML5 FileWriter API will continue to be introduced and at some point will allow us to get rid of the need of a server for local file writing. Certainly what we have now is close to ideal. Check it out at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.17.zip Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] resizable JSmol image is distorted on resize
I can't reproduce your problem at http://chemapps.stolaf.edu/jmol/jsmol/resize.htm Can you? On Tue, Sep 17, 2013 at 5:01 PM, Angel Herráez angel.herr...@uah.es wrote: I don't think this was fixed; it differs with browsers, and those that do not notify of the resize until the mouse is released will do this. What I see (and think I did not see before) is that releasing the mouse still does not do the update, the canvas image stays distorted until I **rotate** the model by dragging inside JSmol. I will research further whether this is a change in behaviour, as I feel. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] resizable JSmol image is distorted on resize
I don't think this was fixed; it differs with browsers, and those that do not notify of the resize until the mouse is released will do this. What I see (and think I did not see before) is that releasing the mouse still does not do the update, the canvas image stays distorted until I **rotate** the model by dragging inside JSmol. I will research further whether this is a change in behaviour, as I feel. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Recommendations for Jmol web hosting
I'd like to publish a few web pages with Jmol applets, but don't necessarily want to use my own computer. Does anyone have a recommendation for a hosting company that supports java applets? Should I be using a signed applet? Thanks -Art - Arthur G. Cox, PhD Associate Professor, Pharmaceutical Sciences South University School of Pharmacy 709 Mall Blvd Savannah, GA 31406 Phone: 912-201-8133 (office), 912-656-0699 (cell) E-Mail: a...@southuniversity.edu -- CONFIDENTIALITY NOTICE: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, you may not review, copy or distribute this message. If you have received this email in error, please notify the sender immediately and delete the original message. Neither the sender nor the company for which he or she works accepts any liability for any damage caused by any virus transmitted by this email. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] resizable JSmol image is distorted on resize
Robert Hanson wrote: I can't reproduce your problem at http://chemapps.stolaf.edu/jmol/jsmol/resize.htm Can you? Coincidence! I was just testing that one. No, that one works fine. Same for my page at http://biomodel.uah.es/en/model3js/monosac.htm But yours says it's using 13.2 and mine has 13.1.15 My current testing is with 13.3 Any chance there is a difference there? Might be critical to have this: !DOCTYPE html html style=height:100% Not exactly. I'm not using resize based on window size. I am using a resizable div that contains JSmol. I will try and prepare test pages tomorrow. Ooops! I'm afraid I haven't got the html5 doctype in those pages. My fault! I'm supposed to know that. Could that be it? More news tomorrow -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] resizable JSmol image is distorted on resize
I don't think this was fixed; it differs with browsers, and those that do not notify of the resize until the mouse is released will do this. On Tue, Sep 17, 2013 at 6:33 AM, Angel Herráez angel.herr...@uah.es wrote: Hi all This is an older problem that was solved and it seems now to be back in JSmol which I downloaded yesterday (jmol-13.3.6_2013.09.14.zip from StOlaf) In the HTML5 mode, when the container is resized (I'm using jQuery resizable for that and 100% Jmol Object), the model image gets distorted until you go and drag the model around again. I'm quite sure this was fixed time ago. I may have a mixture of jQuery versions (my external one and that included by JSmol, but I've been unable to use JSmol.nojq.min.js) but I dont think it should be that since everything else is working fine. Any inspiration, Bob? If you don't have one, I will try to set up test pages -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] error in loading the applet in JSmol
files are missing from jsmol/j2s directory. On Tue, Sep 17, 2013 at 1:49 PM, pino.stricc...@libero.it pino.stricc...@libero.it wrote: Hi Friends, while doing some trials with formatting to float left the applet in JSmol i run into this error when starting the JSmol. Jmol._Canvas2D (JSmol) jmolApplet0[x] call loadScript core\package.js call loadScript core\package.js -- required by w3c script failed What has Happened? Pino -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jsmol -- local file reading/drag drop and local file writing
On Tue, Sep 17, 2013 at 11:59 AM, Otis Rothenberger osrot...@chemagic.comwrote: Bob, I have a biochemist friend doing some testing of the local read/write. It works on my Mac Safari for small molecules. On the write dialog box, is there any way to trap a cancel button before the cancel result hits the server PHP? As it is, a cancel simply generates a PHP error that's automatically saved on Mac/Safari. This will be a bit confusing to users. yes, yes. That got fixed today. I'm still trying to save individual model rotation and conformation rotation on a keyless iPad. I'm stumped. Now that unbind LEFT cuts subsequent drag script binding off also, binding LEFT to a new script will not work for drag related scripts. I can sill bind LEFT to other scripts as long as they do not involve drag. After the unbind LEFT however, the screen is dead to any scripts involving dragging. I have to think about what is going on there Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Sep 16, 2013, at 6:54 PM, Robert Hanson wrote: OK. I have uploaded changes to Jmol that allow JSmol/HTML5 to read and write files to a local drive. Whew! That was tricky -- text, binary, zip, gzip, pngj, xml -- I checked as many as I could find. Please test on a variety of platforms: http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.16.zip top center column -- local file read write Bob ___JmolVersion=13.3.6_dev_2013.09.16 bug fix: chains improperly selected in JSmol/HTML5 bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local drive. bug fix: JSmol/HTML5 not allowing WRITE FILE ? bug fix: platformSpeed persists but appears unreadable after loading a state bug fix: JavaScript version InputStreamReader not processing non-UTF data correctly bug fix: second reading of older PNG files with embedded script fails due to improper png file caching new feature: set drawFontSize // defaults to 14.0 -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Implementation of antialiasing in Jmol
On Tue, Sep 17, 2013 at 2:32 AM, Greg Edwards gedwar...@gmail.com wrote: Hi, I'm interested in the implementation of the antialiasing in Jmol, and I guess whether there are any (undocumented ?) options for controlling the quality. The quality is good, but would be interesting to try the highest quality if there were options. It could be say 2x2 supersampling, ie. render to a framebuffer twice the dimensions of the applet window and reduce down with simple averaging of 4 pixels into 1. Simple but consumes frame buffer space and costs 4x polygon fill load. 2x2 full-scene anti-aliasing is what is implemented in Jmol. Or it could be MultiSample rendering into a dithered grid of subpixel locations, in which case you can have 2, 4, 6, 8 or other numbers of sample points, and there are many choices of the grid of subpixel locations. http://en.wikipedia.org/wiki/Supersample_anti-aliasing http://en.wikipedia.org/wiki/Multisample_anti-aliasing I have an academic/historic interest in this, I worked for SGI for 15 years, during which they introduced the Reality Engine and later models with hardware multisample antialising, and we spent much time working with it, measuring quality and performance in detail. It's all pretty standard now in Nvidia and ATI graphics cards. I'm pretty rusty on the latest developments, apologies if the above is inaccurate. Do you know of some examples of discussion of comparisons of subpixel-sampling vs. supersampling? Whatever we do needs to work with text and translucency. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] resizable JSmol image is distorted on resize
Might be critical to have this: !DOCTYPE htmlhtml style=height:100% Can't remember... On Tue, Sep 17, 2013 at 4:57 PM, Robert Hanson hans...@stolaf.edu wrote: I can't reproduce your problem at http://chemapps.stolaf.edu/jmol/jsmol/resize.htm Can you? On Tue, Sep 17, 2013 at 5:01 PM, Angel Herráez angel.herr...@uah.eswrote: I don't think this was fixed; it differs with browsers, and those that do not notify of the resize until the mouse is released will do this. What I see (and think I did not see before) is that releasing the mouse still does not do the update, the canvas image stays distorted until I **rotate** the model by dragging inside JSmol. I will research further whether this is a change in behaviour, as I feel. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Implementation of antialiasing in Jmol
Thanks Robert. Yes transparency is always a problem, and text too. I did see issues on that in the Jmol mailing list archives. I don;t have any material directly to hand, but will look around. Greg. On 18 September 2013 06:59, Robert Hanson hans...@stolaf.edu wrote: On Tue, Sep 17, 2013 at 2:32 AM, Greg Edwards gedwar...@gmail.com wrote: Hi, I'm interested in the implementation of the antialiasing in Jmol, and I guess whether there are any (undocumented ?) options for controlling the quality. The quality is good, but would be interesting to try the highest quality if there were options. It could be say 2x2 supersampling, ie. render to a framebuffer twice the dimensions of the applet window and reduce down with simple averaging of 4 pixels into 1. Simple but consumes frame buffer space and costs 4x polygon fill load. 2x2 full-scene anti-aliasing is what is implemented in Jmol. Or it could be MultiSample rendering into a dithered grid of subpixel locations, in which case you can have 2, 4, 6, 8 or other numbers of sample points, and there are many choices of the grid of subpixel locations. http://en.wikipedia.org/wiki/Supersample_anti-aliasing http://en.wikipedia.org/wiki/Multisample_anti-aliasing I have an academic/historic interest in this, I worked for SGI for 15 years, during which they introduced the Reality Engine and later models with hardware multisample antialising, and we spent much time working with it, measuring quality and performance in detail. It's all pretty standard now in Nvidia and ATI graphics cards. I'm pretty rusty on the latest developments, apologies if the above is inaccurate. Do you know of some examples of discussion of comparisons of subpixel-sampling vs. supersampling? Whatever we do needs to work with text and translucency. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.[2/3].6 reading/writing - how cool is this?
Bob: On a Mac using the latest OS (10.8.5) Firefox works fine to load and write files; there seems to be no choice where they get downloaded, though I can control that in the browser preferences. I note that the name of the file selected to load is given in the dialog. In Safari there are a couple of issues. The name is not given when the file is chosen. More importantly, we are back to the lines issue. I have cleared the browser cache, and, in fact, disabled it. Perhaps Otis can confirm that glitch?? On Sep 17, 2013, at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: Used to be that it required the signed applet to read and write files locally. Well, well, what do you know? I'm liking HTML5 more and more. The following commands, previously for the signed applet only, now work in JSmol/HTML5. load ? x = load(?) write file ? write xxx.jpg write xxx.png write PNGJ xxx.png write PNGJ 500 500 xxx.png write xxx.zip write xxx.jmol write xxx.pdbwrite xxx.mol write xxx.v2000 write xxx.v3000 write xxx.xyz What's especially satisfying for me is that the loading is done asynchronously. I had thought that would be extremely difficult to do -- to pause a running script of however many levels of depth and deep into however many function calls while an asynchronous file load was happening, then restart upon completion at the right place. Well, guess what? It was only moderately difficult! The HTML5 FileReader API is great. [http://www.w3.org/TR/FileAPI/ ] Looks like this has reasonable support across browsers (http://caniuse.com/#feat=filereader), although one cannot go back very far in time. Writing files to disk still requires reflecting the data from Info.serverUrl, but I'm optimistic (based on http://caniuse.com/filesystem) that the HTML5 FileWriter API will continue to be introduced and at some point will allow us to get rid of the need of a server for local file writing. Certainly what we have now is close to ideal. Check it out at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.17.zip Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.[2/3].6 reading/writing - how cool is this?
Hi Phil, I thought the missing name was normal. When I wrote my friend today, I had to explain that after selecting the file, he had to click the load button! I'm not sure I know what you mean by the lines issue. What am I looking for in Safari with this issue? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Sep 17, 2013, at 6:19 PM, Philip Bays wrote: Bob: On a Mac using the latest OS (10.8.5) Firefox works fine to load and write files; there seems to be no choice where they get downloaded, though I can control that in the browser preferences. I note that the name of the file selected to load is given in the dialog. In Safari there are a couple of issues. The name is not given when the file is chosen. More importantly, we are back to the lines issue. I have cleared the browser cache, and, in fact, disabled it. Perhaps Otis can confirm that glitch?? On Sep 17, 2013, at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: Used to be that it required the signed applet to read and write files locally. Well, well, what do you know? I'm liking HTML5 more and more. The following commands, previously for the signed applet only, now work in JSmol/HTML5. load ? x = load(?) write file ? write xxx.jpg write xxx.png write PNGJ xxx.png write PNGJ 500 500 xxx.png write xxx.zip write xxx.jmol write xxx.pdbwrite xxx.mol write xxx.v2000 write xxx.v3000 write xxx.xyz What's especially satisfying for me is that the loading is done asynchronously. I had thought that would be extremely difficult to do -- to pause a running script of however many levels of depth and deep into however many function calls while an asynchronous file load was happening, then restart upon completion at the right place. Well, guess what? It was only moderately difficult! The HTML5 FileReader API is great. [http://www.w3.org/TR/FileAPI/ ] Looks like this has reasonable support across browsers (http://caniuse.com/#feat=filereader), although one cannot go back very far in time. Writing files to disk still requires reflecting the data from Info.serverUrl, but I'm optimistic (based on http://caniuse.com/filesystem) that the HTML5 FileWriter API will continue to be introduced and at some point will allow us to get rid of the need of a server for local file writing. Certainly what we have now is close to ideal. Check it out at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.17.zip Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.[2/3].6 reading/writing - how cool is this?
Try loading a protein from the right-hand column. What do you see? Remember when we had the odd display of simply lines on the screen several weeks ago? I see it again. You may have to load several structures before the problem shows up. Once it appears, you have to reload the page to get rid of it. Now, I updated the OS today to 10.8.5 and that also updates Safari (6.0.5) so the problem could be there. On Sep 17, 2013, at 7:41 PM, Otis Rothenberger osrot...@chemagic.com wrote: Hi Phil, I thought the missing name was normal. When I wrote my friend today, I had to explain that after selecting the file, he had to click the load button! I'm not sure I know what you mean by the lines issue. What am I looking for in Safari with this issue? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Sep 17, 2013, at 6:19 PM, Philip Bays wrote: Bob: On a Mac using the latest OS (10.8.5) Firefox works fine to load and write files; there seems to be no choice where they get downloaded, though I can control that in the browser preferences. I note that the name of the file selected to load is given in the dialog. In Safari there are a couple of issues. The name is not given when the file is chosen. More importantly, we are back to the lines issue. I have cleared the browser cache, and, in fact, disabled it. Perhaps Otis can confirm that glitch?? On Sep 17, 2013, at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: Used to be that it required the signed applet to read and write files locally. Well, well, what do you know? I'm liking HTML5 more and more. The following commands, previously for the signed applet only, now work in JSmol/HTML5. load ? x = load(?) write file ? write xxx.jpg write xxx.png write PNGJ xxx.png write PNGJ 500 500 xxx.png write xxx.zip write xxx.jmol write xxx.pdbwrite xxx.mol write xxx.v2000 write xxx.v3000 write xxx.xyz What's especially satisfying for me is that the loading is done asynchronously. I had thought that would be extremely difficult to do -- to pause a running script of however many levels of depth and deep into however many function calls while an asynchronous file load was happening, then restart upon completion at the right place. Well, guess what? It was only moderately difficult! The HTML5 FileReader API is great. [http://www.w3.org/TR/FileAPI/ ] Looks like this has reasonable support across browsers (http://caniuse.com/#feat=filereader), although one cannot go back very far in time. Writing files to disk still requires reflecting the data from Info.serverUrl, but I'm optimistic (based on http://caniuse.com/filesystem) that the HTML5 FileWriter API will continue to be introduced and at some point will allow us to get rid of the need of a server for local file writing. Certainly what we have now is close to ideal. Check it out at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.17.zip Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio
Re: [Jmol-users] Jmol 13.[2/3].6 reading/writing - how cool is this?
Phil, OK, I see it on Bob's page. I've been testing on my page at: http://chemistry.illinoisstate.edu/osrothen/JSmolVMK.htm I haven't seen the lines there yet. Try it per the load commands for the script field on the main page: loadpdb searchpdb I'm on Safari 6.0.5 (7536.30.1) I haven't yet document the read/write commands, but the are loadloc saveloc Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Sep 17, 2013, at 8:05 PM, Bays Philip wrote: Try loading a protein from the right-hand column. What do you see? Remember when we had the odd display of simply lines on the screen several weeks ago? I see it again. You may have to load several structures before the problem shows up. Once it appears, you have to reload the page to get rid of it. Now, I updated the OS today to 10.8.5 and that also updates Safari (6.0.5) so the problem could be there. On Sep 17, 2013, at 7:41 PM, Otis Rothenberger osrot...@chemagic.com wrote: Hi Phil, I thought the missing name was normal. When I wrote my friend today, I had to explain that after selecting the file, he had to click the load button! I'm not sure I know what you mean by the lines issue. What am I looking for in Safari with this issue? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Sep 17, 2013, at 6:19 PM, Philip Bays wrote: Bob: On a Mac using the latest OS (10.8.5) Firefox works fine to load and write files; there seems to be no choice where they get downloaded, though I can control that in the browser preferences. I note that the name of the file selected to load is given in the dialog. In Safari there are a couple of issues. The name is not given when the file is chosen. More importantly, we are back to the lines issue. I have cleared the browser cache, and, in fact, disabled it. Perhaps Otis can confirm that glitch?? On Sep 17, 2013, at 5:54 PM, Robert Hanson hans...@stolaf.edu wrote: Used to be that it required the signed applet to read and write files locally. Well, well, what do you know? I'm liking HTML5 more and more. The following commands, previously for the signed applet only, now work in JSmol/HTML5. load ? x = load(?) write file ? write xxx.jpg write xxx.png write PNGJ xxx.png write PNGJ 500 500 xxx.png write xxx.zip write xxx.jmol write xxx.pdbwrite xxx.mol write xxx.v2000 write xxx.v3000 write xxx.xyz What's especially satisfying for me is that the loading is done asynchronously. I had thought that would be extremely difficult to do -- to pause a running script of however many levels of depth and deep into however many function calls while an asynchronous file load was happening, then restart upon completion at the right place. Well, guess what? It was only moderately difficult! The HTML5 FileReader API is great. [http://www.w3.org/TR/FileAPI/ ] Looks like this has reasonable support across browsers (http://caniuse.com/#feat=filereader), although one cannot go back very far in time. Writing files to disk still requires reflecting the data from Info.serverUrl, but I'm optimistic (based on http://caniuse.com/filesystem) that the HTML5 FileWriter API will continue to be introduced and at some point will allow us to get rid of the need of a server for local file writing. Certainly what we have now is close to ideal. Check it out at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.6_2013.09.17.zip Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud,
Re: [Jmol-users] Recommendations for Jmol web hosting
Hi Arthur, If you are a GitHub user, I found GitHub works just fine using GitHub Pages feature, see http://pages.github.com/. It is free and linked to your project. It says it is for 'static sites' but apparently Java-based sites count under that. You'll need the signed applet if you are going to be getting the structure file from another server though. Otherwise the unsigned works. You can even host JSmol sites there if you include the structure file. I haven't figured out if it is possible to get the cross domain file fetching to work there because I don't know if the php runs. The only time I tried it didn't work. But it turned out it was not a fair test. It was a complex site I was trying to adapt with little effort and loading a structure file from the PDB didn't work when I finally tried it on a server where I was pretty sure php was working. I need to test loading from another server with JSmol on GitHub Pages using Bob's test files at some point. I fear though running php code takes it out of the 'static sites' realm. Anybody else tried hosting JSmol pages yet at GitHub and grabbed files from elsewhere? Wayne -- Message: 3 Date: Tue, 17 Sep 2013 17:42:54 -0400 From: Cox, Arthur G. a...@southuniversity.edu Subject: [Jmol-users] Recommendations for Jmol web hosting To: jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.net Message-ID: 0ba1ecc2eb8dfb4cb303ae33d566fd940a88a4d...@csexcmsadm02.admin.edmc.adm Content-Type: text/plain; charset=us-ascii I'd like to publish a few web pages with Jmol applets, but don't necessarily want to use my own computer. Does anyone have a recommendation for a hosting company that supports java applets? Should I be using a signed applet? Thanks -Art - Arthur G. Cox, PhD Associate Professor, Pharmaceutical Sciences South University School of Pharmacy 709 Mall Blvd Savannah, GA 31406 Phone: 912-201-8133 (office), 912-656-0699 (cell) E-Mail: a...@southuniversity.edu-- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Recommendations for Jmol web hosting
Art, Have you considered http://proteopedia.org ? Jaim On Sep 18, 2013, at 12:42 AM, Cox, Arthur G. wrote: I'd like to publish a few web pages with Jmol applets, but don't necessarily want to use my own computer. Does anyone have a recommendation for a hosting company that supports java applets? Should I be using a signed applet? Thanks -Art - Arthur G. Cox, PhD Associate Professor, Pharmaceutical Sciences South University School of Pharmacy 709 Mall Blvd Savannah, GA 31406 Phone: 912-201-8133 (office), 912-656-0699 (cell) E-Mail: a...@southuniversity.edu -- CONFIDENTIALITY NOTICE: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, you may not review, copy or distribute this message. If you have received this email in error, please notify the sender immediately and delete the original message. Neither the sender nor the company for which he or she works accepts any liability for any damage caused by any virus transmitted by this email. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] iPad Key Modified Drag
Bob, I got it. It was native to JSmol all along. On an iPad, all I needed was way to have a drag AND a key modified drag binding. The Jmol default for DOUBLE is click-click-drag to translate. In JSmol, click-click-drag can be bound (bind DOUBLE) to other drag scripts that work on an iPad and a desktop with all the drag related _VARIABLES working. When you do this, click-drag and click-click-drag live happily together on the same model screen working independently. It's as if that first click is equivalent to a keyboard modifier. Exactly what I needed on an iPad. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Fwd: Recommendations for Jmol web hosting
(Previous send of this failed, due to too-large inline image of bucket layout. Moderator, discard previous pls.) Arthur, I'm using an Amazon AWS S3 bucket. This is extremely cheap, 99.9% reliable. Try .. http://jmolwork2.s3.amazonaws.com/section1/caffeine-nogui.html http://jmolwork2.s3.amazonaws.com/section1/index_orig_demo.html I'm using the unsigned applet. Structure is .. http://jmolwork2.s3.amazonaws.com/images/bucket-layout.png Models are local in models. Html files in section1. Works on Mac SL/10.6.8 M/10.8.4, Chrome, Firefox, Safari, Chrome. Windows 7 + Chrome. Not sure IE has been tried :=( I will write this up on the Wiki soon I think, as an up-to-date example for beginners. Let me know if you would like more detail. Cheers, Greg On 18 September 2013 07:42, Cox, Arthur G. a...@southuniversity.edu wrote: I'd like to publish a few web pages with Jmol applets, but don't necessarily want to use my own computer. Does anyone have a recommendation for a hosting company that supports java applets? Should I be using a signed applet? Thanks -Art - Arthur G. Cox, PhD Associate Professor, Pharmaceutical Sciences South University School of Pharmacy 709 Mall Blvd Savannah, GA 31406 Phone: 912-201-8133 (office), 912-656-0699 (cell) E-Mail: a...@southuniversity.edu -- CONFIDENTIALITY NOTICE: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, you may not review, copy or distribute this message. If you have received this email in error, please notify the sender immediately and delete the original message. Neither the sender nor the company for which he or she works accepts any liability for any damage caused by any virus transmitted by this email. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
