[Jmol-users] Definitions
These questions may have already been addressed. If so, just point me in the right direction. Can someone clarify the meaning of the following terms in the context of the new Jmol/JSmol? Jmol JSmol Applet Jmol script JSmol script These terms are used in context on this list, and the meaning is usually apparent to list followers even though the terms are being used inconsistently. Communication with non-list followers, however, can get confusing. Are there other terms that need clarification? Are there new terms that should be created? I'm working on a JCE paper, and I just realized that I didn't know what I was talking about! I believe Bob has said that there really only is Jmol. I understand what he's saying with this, but that still leaves some term confusion. Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Definitions
On 5 Jan 2014, at 14:36, Otis Rothenberger osrot...@chemagic.com wrote: These questions may have already been addressed. If so, just point me in the right direction. Can someone clarify the meaning of the following terms in the context of the new Jmol/JSmol? Jmol JSmol Applet Jmol script JSmol script There is also the historic Rasmol script (RAS = Roger A Sayle), which I believe is synonymous with Jmol and JSmol script. Roger of course contributed Rasmol, of which a fair bit of code was probably used in the original versions of Jmol. In case any on this list do not know the history, prior to ~1991, the idea of real time rendered rotation of large biomolecular structures on a mere “personal computer” was considered a fantasy; you needed a “real graphics workstation” to do this, if not an Evans and Sutherland, then certainly a Silicon Graphics. It was Rasmol that changed all of that.It was also Rasmol that was first deployed on a Web page (you may know that instance as Chime, but that was really Rasmol). signature.asc Description: Message signed with OpenPGP using GPGMail -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Definitions
On Jan 5, 2014, at 9:57 am, Rzepa, Henry S wrote: On 5 Jan 2014, at 14:36, Otis Rothenberger osrot...@chemagic.com wrote: These questions may have already been addressed. If so, just point me in the right direction. Can someone clarify the meaning of the following terms in the context of the new Jmol/JSmol? Jmol JSmol Applet Jmol script JSmol script There is also the historic Rasmol script (RAS = Roger A Sayle), which I believe is synonymous with Jmol and JSmol script. Roger of course contributed Rasmol, of which a fair bit of code was probably used in the original versions of Jmol. yes, the Jmol scripting language was derived directly from RAS. it has, of course, evolved considerably since then. :-D conceptually, the Rasmol software definitely inspired Jmol. actually, from my perspective it was the closed-source nature of Chime that really got the Jmol ball rolling. strictly speaking, however, I don't recall any actual Rasmol code being migrated, since Rasmol was written in C and Jmol in Java. I imagine Miguel Howard would be the definitive authority on this topic, though it's likely that Bob would know, too. I only point this out because OP confessed to writing a manuscript, and it's probably good to be clear on this point in any publication. happy new year, tim -- timothy driscoll, phd bioinformatician cyberinfrastructure division virgina bioinformatics institute -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Definitions
yes, the Jmol scripting language was derived directly from RAS. it has, of course, evolved considerably since then. :-D conceptually, the Rasmol software definitely inspired Jmol. actually, from my perspective it was the closed-source nature of Chime that really got the Jmol ball rolling. strictly speaking, To the best of my recollection, Rasmol itself was open. MDL acquired this open source code and “wrapped it” into a closed-code Chime (I think they added data-base querying code which was proprietary to them). A third party involved was Glaxo, for whom Roger worked at the time. Only the MDL and Glaxo lawyers know exactly what the arrangement between them was. The connection between MDL/Chime and Netscape (who had written the browser plug-in architecture that Chime made use of) was partly geographical ( 30 km) and partly an article I had written (so its developers told me). however, I don't recall any actual Rasmol code being migrated, since Rasmol was written in C and Jmol in Java. I meant that presumably many of the algorithms, including the rendering code, were re-written into Java. I imagine Miguel Howard would be the definitive authority on this topic, though it's likely that Bob would know, too. signature.asc Description: Message signed with OpenPGP using GPGMail -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Definitions
Here's my two cents on this topic: Jmol JSmol Applet Jmol script JSmol script Certainly no reason to talk about a JSmol script. The command language is the same, so Jmol script (Jmol scripting language) is enough. Applet is a term I am tryng to avoid now, unless one is specifically talking abut the Java modality. I realize it is being used a lot when talking about the new J(S)mol, but this will be confusing to many people, particularly if they don't know the story. So I advocate for the systematic use of the term Jmol Object, which may involve either a Java applet (JmolApplet) or an HTML5 entity --rather a set of entities maybe-- mainly built around the canvas tag. In the Jmol Wiki I have tried to use object systematically. When the new method for inserting Jmol into a webpage was created, it was called Jmol-JSO, for Jmol JavaScript Object. This was, and still is, fathful to the mechanism how the object is created, inserted in the page and addressed e.g. by GUI controls. After exploration of several alternatives, what I've come to call modalities of Jmol (Java applet, WebGL object, image, ChemDoodle WebComponent, finally set towards a generic HTML5 canvas) later derived towards the HTML5 modality, and JSmol appeared when the way to port the Jmol Java code into JavaScript was discovered-developed. So JSmol became the colloquial term and is more specific just for the HTML5 variety or modality. The major difference between this and the other candidates is that there is no need to translate commands and procedures to another language, being the same Jmol source code and hence the full functionality of Jmol is achieved. Therefore I would summarize: Jmol = a + b + c a = Jmol application (stand-alone Java program) b = Jmol Object embedded in a webpage = either applet or HTML5 modalities c = Jmol as a library or component to be integrated by developers as part of larger software pieces JSmol = HTML5 modality of a Jmol Object in a webpage Jmol-JSO is the JavaScript code that inserts the Jmol Object into the page (more or less the same that was done before with Jmol.js). That is used for introducing either a JmolApplet or a JSmol object, using the same system and just a change in one variable or parameter. So pages may be easily made dual Java / nonJava, or Jmol/JSmol if you prefer. As far as I have read, the source code of Jmol either evolved from that of Xmol or was written to reproduce its functionality. I don't think there is any direct relationship to Rasmol source code. What Miguel did -among other things- was to expand or build the Jmol scripting language to accept the existing commands in the Rasmol scripting language, in order to bring Jmol as an alternative/successor to Chime, that is, to easily convert pages from using Chime + Rasmol Scripts to using JmolApplet + Jmol Scripts, hence rescuing the large number of Chime-based pages from dying in the dawn of Chime compatibility with new browsers. Finally, although I don't know the details, there is the classic Rasmol and the OpenRasmol, which inherited from the first but was given a separate name and space, so there must be some question about openness of source code in the old Rasmol. I believe that Jmol Scripting came from the classic Rasmol, before the OpenRasmol branch separated (as deduced from version numbers in the Rasmol scripting language documentation). I believe Bob has said that there really only is Jmol. Yes. To me, the key point for that assertion is that there is a single source code. That is then on one hand compiled (?) and packed into a Java applet and on the other hand compiled-translated into JavaScript, to produce, in the released package, filesets for the 2 modalities. -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Definitions
I'll chime in here as well Jmol JSmol Applet Jmol script JSmol script also: signed unsigned all-permissions sandboxed *Jmol/JSmol:* As Angel says, I see them as the same. So to be specific, I recommend using either one with /HTML5, /Java, /WebGL: Jmol/HTML5vs. JSmol/HTML5 Jmol/Javavs. JSmol/Java sound about the same to me. *Applet/Object:* I agree that applet is ambiguous now. What do we call this JavaScript equivalent of a Java applet? In JSmol there is an object, and that object is a true JavaScript object, such as myJmol. In the JSmol library code this is still referred to as an applet though. That page-level object is a wrapper for the Java or JavaScript-equivalent myJmol._applet, which is either a JavaScript object or a Java object. *Jmol script/JSmol script:* Please use Jmol script. *signed/unsigned* *all-permissions/sandboxed* Relevant only for Jmol/Java. More complications here. We need to drop discussion of signed/unsigned and go for all-permissions/sandboxed, as all applets starting in 2014 must be signed. old/new: unsigned/sandboxed Java applet signed/all-permissions Java applet That said, we still have ?_USE=SIGNED meaning all-permissions Java applet 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] FirstGlance in JSmol released
I have today released a new version (1.98) at http://FirstGlance.Jmol.Org This version defaults to using the signed Jmol Java applet 14.0.3, but optionally can use JSmol. At the above URL you will see a pre-checked Use Java checkbox. Unchecking that makes it use JSmol. If you start FirstGlance from a link (such as those in Nature) for example http://FirstGlance.Jmol.Org/fg.htm?mol=1d66 it will default to Jmol/Java, but you will see a prominent Try FirstGlance without Java link. That link will disappear automatically if loading is successful, but you can get it back by clicking on No Java? or Can't see the molecule?. Or you can add nojava or html5 (equivalent), e.g. http://FirstGlance.Jmol.Org/fg.htm?mol=1d66nojava I have tested it in MAC OS 10.6.8 and OS 10.8.5 in Safari, Firefox, Chrome, Opera; and in Windows 7 in Internet Explorer 11, Firefox, Chrome, Opera. All work with both Jmol and JSmol. Internet Explorer 11 is unusably slow with JSmol. So if you uncheck Use Java in Internet Explorer on Windows, a yellow banner appears urging you to use another browser. Unfortunately, on an iPad, Safari vaporizes a couple of seconds after the molecule appears. To be investigated. I am very impressed with how well JSmol works! Major, major kudos to Bob and everyone who has contributed to it!! There are some bugs and limitations that I will report later. Notably, with 20 NMR models (2bbn) the browser tends to freeze. Rotation gets sluggish with 7ahl (over 2,000 atoms) but it is still so much better than nothing! Eric -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 14.x.4 released
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.4 Not much here, but one important fix for ribbons, so if you do anything with proteins be sure to download this modification in 14.0 and 14.1. 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.x.4 released
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.4 Not much here, but one important fix for ribbons, so if you do anything with proteins be sure to download this modification in 14.0 and 14.1. Bob Thank you. Fixed the misplaced rockets elements. PSE conversion works smooth, no problems reported at http://ispcsrv.weizmann.ac.il/a2jmolb/browse Best Regards, Jaim -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
