Re: [Jmol-users] Selecting Atoms with the mouse
Hmm. Yes. And just "Jmol" comes right up with http://jmol.sourceforge.net/docs/ which points directly to the interactive documentation. So I think we are doing about as well as we can on that front. Don't know what the problem was. Bob 2012/1/31 Herráez Sánchez Ángel > I guess it all depends on what serach terms are used. > > I just entered > Jmol documentation > into Google and there it is! > Attached screenshot > > > > > -- > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Selecting Atoms with the mouse
Angel, I think the problem is that Google is not picking it up somehow. We need the link on whatever pages Google is sending people to. 2012/1/31 Angel Herráez > Hi again Ted > > > I certainly was missing that documentation all together. > > To my mind, the offical documentation was rooted at > > http://jmol.sourceforge.net/ > > That did not particulary direct me to the documentation at stolaf.eduthat I > > can recall. > > Perhaps it does and I missed it. > > Let's see, Ted. If you still think that route is not clear, please > advice to impove it. This is what we have: > > Jmol main website: http://jmol.org > (which leads to http://jmol.sourceforge.net/ ) > > Top-right menu: "Documentation" > then: "Scripting for Jmol > Scripting Documentation" > "This interactive online documentation is the reference guide for all > commands ..." > > > Back to home page, down the page: > "Learn to use Jmol > Manuals and tutorials" > "Finally, there is a documentation section in this web site, for more > technical details." > > > > Is that not clear? If you did not find it, maybe others won't wither. > Please suggest. > > > > > There is another issue that I think confronts most new users and that > > is the relationship in Jmol between Java (and the java plugin provided > by each > > browser publisher), Jmol Scripting (with it's > > historical relationship with Chime and Rasmol Scripting) and the > > Javascript interface. One can easily get confused when reading > documentation > > and you don't have a grip on which context the documentation is written > for. > > You might be right. This is not an easy issue. Again, suggestions are > welcome, as well as collaboration. I feel that Jmol documentation is > to a lower standard than Jmol features; that's due to lack of > manpower --or womanpower. I do what I can in that respect. It's hard > to match the coding developers efficiency ;-) > > 1. "most new users" should not need to worry about Java (other than > having it installed o their computer). There is nothing involving the > Java language. > > 2. The Javascript interface is a way to more easily insert and access > Jmol applets and pass to it the scripting language. > > 3. The scripting is th part one must learn by study and testing, and > where all the power of Jmol is. But still quite a few things can be > achieved with very little scripting, for basic display. Then you > quickly grow greedy :) and MUST learn the language! > > > > I have been spending most of my time in the javascript interface which I > think > > is documented at the sourceforge site rather than the stolaf site > > That's right, because it is just so, an interface. To the scripting. > > > > interface looses most of it's power if I don't understand what's on the > otherside > > of it and available in the Jmol Scripting context. It seems like two > seperate worlds > > with two pretty seperate sets of documentation, but to use the full > power of Jmol > > I need to know both and I need to not be confused about what is a > javascript interface > > method and what is a Jmol scripting function (if I even have that > nomenclature correct). > > Yes you have. Every Javascipt function (or call) takes a "script" > argument. That's the link between both "worlds". You have the > steering wheel and the pedals, but then there is the engine hidden > somewhere under the trunk :) > > I'd guess that different people learn Jmol in different ways. > > > Ah, there another little mentioned but worthy tool: the Export to Web > interface included in the Jmol application. It lets you play in Jmol, > menu and scripting, and then produces a basic webpage for you that > includes what you have done. > > > > > -- > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d__
Re: [Jmol-users] Selecting Atoms with the mouse
Hi again Ted > I certainly was missing that documentation all together. > To my mind, the offical documentation was rooted at > http://jmol.sourceforge.net/ > That did not particulary direct me to the documentation at stolaf.edu that I > can recall. > Perhaps it does and I missed it. Let's see, Ted. If you still think that route is not clear, please advice to impove it. This is what we have: Jmol main website: http://jmol.org (which leads to http://jmol.sourceforge.net/ ) Top-right menu: "Documentation" then: "Scripting for Jmol > Scripting Documentation" "This interactive online documentation is the reference guide for all commands ..." Back to home page, down the page: "Learn to use Jmol > Manuals and tutorials" "Finally, there is a documentation section in this web site, for more technical details." Is that not clear? If you did not find it, maybe others won't wither. Please suggest. > There is another issue that I think confronts most new users and that > is the relationship in Jmol between Java (and the java plugin provided by each > browser publisher), Jmol Scripting (with it's > historical relationship with Chime and Rasmol Scripting) and the > Javascript interface. One can easily get confused when reading documentation > and you don't have a grip on which context the documentation is written for. You might be right. This is not an easy issue. Again, suggestions are welcome, as well as collaboration. I feel that Jmol documentation is to a lower standard than Jmol features; that's due to lack of manpower --or womanpower. I do what I can in that respect. It's hard to match the coding developers efficiency ;-) 1. "most new users" should not need to worry about Java (other than having it installed o their computer). There is nothing involving the Java language. 2. The Javascript interface is a way to more easily insert and access Jmol applets and pass to it the scripting language. 3. The scripting is th part one must learn by study and testing, and where all the power of Jmol is. But still quite a few things can be achieved with very little scripting, for basic display. Then you quickly grow greedy :) and MUST learn the language! > I have been spending most of my time in the javascript interface which I think > is documented at the sourceforge site rather than the stolaf site That's right, because it is just so, an interface. To the scripting. > interface looses most of it's power if I don't understand what's on the > otherside > of it and available in the Jmol Scripting context. It seems like two seperate > worlds > with two pretty seperate sets of documentation, but to use the full power of > Jmol > I need to know both and I need to not be confused about what is a javascript > interface > method and what is a Jmol scripting function (if I even have that > nomenclature correct). Yes you have. Every Javascipt function (or call) takes a "script" argument. That's the link between both "worlds". You have the steering wheel and the pedals, but then there is the engine hidden somewhere under the trunk :) I'd guess that different people learn Jmol in different ways. Ah, there another little mentioned but worthy tool: the Export to Web interface included in the Jmol application. It lets you play in Jmol, menu and scripting, and then produces a basic webpage for you that includes what you have done. -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Selecting Atoms with the mouse
On Mon, January 30, 2012 18:11, Robert Hanson wrote: > Ted, maybe you are missing the significance of > http://chemapps.stolaf.edu/jmol/docs Sorry about that! > > This is the official full all-inclusive description of Jmol scripting. Most > people, I think, load that page and then use their browser to search for > various items of interest. If you find something missing there, please do > let me know. I certainly was missing that documentation all together. To my mind, the offical documentation was rooted at http://jmol.sourceforge.net/ That did not particulary direct me to the documentation at stolaf.edu that I can recall. Perhaps it does and I missed it. There is another issue that I think confronts most new users and that is the relationship in Jmol between Java (and the java plugin provided by each browser publisher), Jmol Scripting (with it's historical relationship with Chime and Rasmol Scripting) and the Javascript interface. One can easily get confused when reading documentation and you don't have a grip on which context the documentation is written for. I have been spending most of my time in the javascript interface which I think is documented at the sourceforge site rather than the stolaf site but the javascript interface looses most of it's power if I don't understand what's on the otherside of it and available in the Jmol Scripting context. It seems like two seperate worlds with two pretty seperate sets of documentation, but to use the full power of Jmol I need to know both and I need to not be confused about what is a javascript interface method and what is a Jmol scripting function (if I even have that nomenclature correct). -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Selecting Atoms with the mouse
Ted, maybe you are missing the significance of http://chemapps.stolaf.edu/jmol/docs Sorry about that! This is the official full all-inclusive description of Jmol scripting. Most people, I think, load that page and then use their browser to search for various items of interest. If you find something missing there, please do let me know. Bob Hanson -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Selecting Atoms with the mouse solved
> Using the menus: > 1) Jmol->Main Menu->Select->Selection Halos > 2) Jmol->Main Menu->Select->None > 3) Jmol->Main Menu->Set picking->Select Atom Yes, of course. Points 1 & 2 could be programmed into the page source if you don't want to do them every time jmolApplet(300, "load myFile.mol;select none;set selectionHalos on;") or even 1,2,3: jmolApplet(300, "load myFile.mol;select none;set selectionHalos on;set picking select atom;") :-) <>-- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Selecting Atoms with the mouse solved
On Mon, January 30, 2012 16:44, Herráez Sánchez Ángel wrote: > Hi Ted > > 1. > The popup menu has an entry named "set picking" > That should do what you want. > > There is a "set picking" command too. If you look up the documentation for > that, you can see how it works. > > 2. > Given that the default is to start wirh all selected, maybe you want to > deselect all by including this command in your jmolApplet() call in the page: > > select none; > > I hope that's enough. > Good luck! Thanks Angel. That was enough. Here is the recipe that I came up with using your direction: Using the menus: 1) Jmol->Main Menu->Select->Selection Halos 2) Jmol->Main Menu->Select->None 3) Jmol->Main Menu->Set picking->Select Atom At that point the mouse click works as hoped. Click an atom once to select, again to deselect. The halos let me know the current selection state of each atom and the count in parenthesis after the Select in Jmol->Main Menu gives me a count of the number of atoms selected. -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Selecting Atoms with the mouse
Hi Ted 1. The popup menu has an entry named "set picking" That should do what you want. There is a "set picking" command too. If you look up the documentation for that, you can see how it works. 2. Given that the default is to start wirh all selected, maybe you want to deselect all by including this command in your jmolApplet() call in the page: select none; I hope that's enough. Good luck! <>-- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
