Re: [Jmol-developers] serious refactoring of Jmol
yes, and I'd like some of your stuff, as well, Dean, to display. Anything you can offer in terms of free-running symmetry scripts would be fabulous. I'll be helping to coordinate the small-molecule animation/script additions to the database, so let me know if you want anything. Others -- speaking of which, if you have small-molecule or crystallographic scripts that you would like to contribute, just say the word. Bob On Thu, Sep 29, 2011 at 2:55 PM, Dean Johnston djohnsto...@gmail.comwrote: Is there anywhere to get more details info (source, binaries) for the Molecular Playground setup? I looked at the web site, but the details are sparse. I'd love to set something like this up here. Dean On Tue, Sep 27, 2011 at 2:02 PM, Jonathan Gutow gu...@uwosh.edu wrote: This looks cool...I'm going to see if I can convince my School to set something up. Jonathan On Sep 27, 2011, at 10:55 AM, Robert Hanson wrote: Over the past few days I've been doing some major refactoring of Jmol 12. The changes should be transparent, but the overall effect should be significant. All core java.awt and java.swing references are now made from within org.jmol.awt or org.jmol.export (where all the file dialogs are). org.jmol.console, org.jmol.modelkit, and org.jmol.viewer.MouseManager14.java (now Mouse.java) have all been moved into org.jmol.awt. This is in preparation for Mario Kosmiskas integrating his Jmol Android and NET apps into core Jmol. Both Android and NET will be separate Java/C## projects (within the Jmol Sourceforge project) that link to the Jmol project, so developers not interested in those won't need the Android SDK. In addition, I've been working with Adam Williams at U-Mass Amherst on adding JSON-protocol NIO socket and kiosk capability to the Jmol app. What this means is that you will be able to start Jmol in kiosk mode, which basically makes the application look like the applet (an undecorated black square) that can be projected onto a wall. By specifying a port number on the Jmol command line, you will be able to communicate with Jmol via that port essentially like applets communicate with each other using SYNC commands. Adam has written a Kinect-driven host that takes this Jmol app as its client. Jmol listens asynchronously on the port for raw mouse motions, script commands, and SYNC messages using a simple JSON protocol, and reports back to the host when a script has completed. Adam has installed this at U-Mass Amherst as the Molecular Playground http://molecularPlayground.org and we are currently installing a version of this at St. Olaf. So maybe the theme for the week is from small to large -- Jmol on cell phones and in public spaces. Bob -- 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1
Re: [Jmol-developers] serious refactoring of Jmol
Dean, Craig Martin at U-Mass/Amherst is the brains behind this. We're just now getting it set up and actually totally integrated into Jmol now. It's two pieces -- the Jmol side and the server/Kinect side. The latter is available as compiled Mac binary -- so far this needs a Mac to run -- but just ask Craig about it. Bob On Thu, Sep 29, 2011 at 2:55 PM, Dean Johnston djohnsto...@gmail.comwrote: Is there anywhere to get more details info (source, binaries) for the Molecular Playground setup? I looked at the web site, but the details are sparse. I'd love to set something like this up here. Dean On Tue, Sep 27, 2011 at 2:02 PM, Jonathan Gutow gu...@uwosh.edu wrote: This looks cool...I'm going to see if I can convince my School to set something up. Jonathan On Sep 27, 2011, at 10:55 AM, Robert Hanson wrote: Over the past few days I've been doing some major refactoring of Jmol 12. The changes should be transparent, but the overall effect should be significant. All core java.awt and java.swing references are now made from within org.jmol.awt or org.jmol.export (where all the file dialogs are). org.jmol.console, org.jmol.modelkit, and org.jmol.viewer.MouseManager14.java (now Mouse.java) have all been moved into org.jmol.awt. This is in preparation for Mario Kosmiskas integrating his Jmol Android and NET apps into core Jmol. Both Android and NET will be separate Java/C## projects (within the Jmol Sourceforge project) that link to the Jmol project, so developers not interested in those won't need the Android SDK. In addition, I've been working with Adam Williams at U-Mass Amherst on adding JSON-protocol NIO socket and kiosk capability to the Jmol app. What this means is that you will be able to start Jmol in kiosk mode, which basically makes the application look like the applet (an undecorated black square) that can be projected onto a wall. By specifying a port number on the Jmol command line, you will be able to communicate with Jmol via that port essentially like applets communicate with each other using SYNC commands. Adam has written a Kinect-driven host that takes this Jmol app as its client. Jmol listens asynchronously on the port for raw mouse motions, script commands, and SYNC messages using a simple JSON protocol, and reports back to the host when a script has completed. Adam has installed this at U-Mass Amherst as the Molecular Playground http://molecularPlayground.org and we are currently installing a version of this at St. Olaf. So maybe the theme for the week is from small to large -- Jmol on cell phones and in public spaces. Bob -- 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net
Re: [Jmol-developers] serious refactoring of Jmol
Is there anywhere to get more details info (source, binaries) for the Molecular Playground setup? I looked at the web site, but the details are sparse. I'd love to set something like this up here. Dean On Tue, Sep 27, 2011 at 2:02 PM, Jonathan Gutow gu...@uwosh.edu wrote: This looks cool...I'm going to see if I can convince my School to set something up. Jonathan On Sep 27, 2011, at 10:55 AM, Robert Hanson wrote: Over the past few days I've been doing some major refactoring of Jmol 12. The changes should be transparent, but the overall effect should be significant. All core java.awt and java.swing references are now made from within org.jmol.awt or org.jmol.export (where all the file dialogs are). org.jmol.console, org.jmol.modelkit, and org.jmol.viewer.MouseManager14.java (now Mouse.java) have all been moved into org.jmol.awt. This is in preparation for Mario Kosmiskas integrating his Jmol Android and NET apps into core Jmol. Both Android and NET will be separate Java/C## projects (within the Jmol Sourceforge project) that link to the Jmol project, so developers not interested in those won't need the Android SDK. In addition, I've been working with Adam Williams at U-Mass Amherst on adding JSON-protocol NIO socket and kiosk capability to the Jmol app. What this means is that you will be able to start Jmol in kiosk mode, which basically makes the application look like the applet (an undecorated black square) that can be projected onto a wall. By specifying a port number on the Jmol command line, you will be able to communicate with Jmol via that port essentially like applets communicate with each other using SYNC commands. Adam has written a Kinect-driven host that takes this Jmol app as its client. Jmol listens asynchronously on the port for raw mouse motions, script commands, and SYNC messages using a simple JSON protocol, and reports back to the host when a script has completed. Adam has installed this at U-Mass Amherst as the Molecular Playground http://molecularPlayground.org and we are currently installing a version of this at St. Olaf. So maybe the theme for the week is from small to large -- Jmol on cell phones and in public spaces. Bob -- 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] serious refactoring of Jmol
I'll see what I can come up with symmetry-wise. We were just playing around with some Spartan animations (vibrations) of ferrocene today - I think those would make for some nice demos. Dean On Thu, Sep 29, 2011 at 4:02 PM, Robert Hanson hans...@stolaf.edu wrote: yes, and I'd like some of your stuff, as well, Dean, to display. Anything you can offer in terms of free-running symmetry scripts would be fabulous. I'll be helping to coordinate the small-molecule animation/script additions to the database, so let me know if you want anything. Others -- speaking of which, if you have small-molecule or crystallographic scripts that you would like to contribute, just say the word. Bob On Thu, Sep 29, 2011 at 2:55 PM, Dean Johnston djohnsto...@gmail.comwrote: Is there anywhere to get more details info (source, binaries) for the Molecular Playground setup? I looked at the web site, but the details are sparse. I'd love to set something like this up here. Dean -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] serious refactoring of Jmol
On behalf of Craig Martin: -- Forwarded message -- From: Dean Johnston djohnsto...@gmail.com Date: Thu, Sep 29, 2011 at 2:55 PM Subject: Re: [Jmol-developers] serious refactoring of Jmol To: jmol-developers@lists.sourceforge.net Is there anywhere to get more details info (source, binaries) for the Molecular Playground setup? I looked at the web site, but the details are sparse. I'd love to set something like this up here. Dean Thanks for your interest in the Molecular Playground and YES, we definitely want to encourage other installations (there are four currently either in production or undergoing installation as we speak). This project was funded by a grant from the Camille Henry Dreyfus Foundation, with the specific intent of fostering installations around the country/world. The hardware costs for your own Playground are minimal: $150 Kinect Device (an XBox peripheral) $700 Mac Mini (any reasonably recent Macintosh computer will do) $ ?? Projector (here costs could range from $300 to $6,000, depending on your local requirements - ambient light, etc) The setup then just requires mounting, electrical, and internet connection. Other than the physical requirements of your specific mounting, setting up a Playground is very easy. Please visit http://MolecularPlayground.orghttp://molecularplayground.org/ for more information We're currently working on placing a downloadable package there, complete with instructions. Stay tuned to that site. If you're impatient and want to start playing immediately, contact me directly. Note that you'll be able to play with this as a one shot, if you already have or can borrow the hardware above. Put the projector and Kinect on a table or step-ladder and point it at a wall. I've already had a colleague take a setup to a conference to demonstrate the system. Finally, for those who don't know what this is, the Molecular Playground is an interactive exhibit that allows passersby to play with molecules projected on a wall (driven by Jmol, of course!). A simple wave of the arm will allow users to take control of and rotate the molecule, for example. We've had one up and running at UMass for two years now and it's received a lot of favorable attention. Individual installations will be able to choose their own playlist of molecules from a database here at UMass. We are also looking for submissions of content (content submission will be available from the above WEB site as well - soon, we hope!). So Jmol developers take note - we hope for great things from you all! Sincerely, Craig T. Martin Professor of Chemistry Adjunct Professor of Biochemistry and Molecular Biology Member Program in Molecular Cellular Biology Department of Chemistry Lederle Graduate Research Tower, Room 104 University of Massachusetts 710 N Pleasant St. Amherst, MA 01003 cmar...@chem.umass.edu On Thu, Sep 29, 2011 at 2:55 PM, Dean Johnston djohnsto...@gmail.comwrote: Is there anywhere to get more details info (source, binaries) for the Molecular Playground setup? I looked at the web site, but the details are sparse. I'd love to set something like this up here. Dean On Tue, Sep 27, 2011 at 2:02 PM, Jonathan Gutow gu...@uwosh.edu wrote: This looks cool...I'm going to see if I can convince my School to set something up. Jonathan On Sep 27, 2011, at 10:55 AM, Robert Hanson wrote: Over the past few days I've been doing some major refactoring of Jmol 12. The changes should be transparent, but the overall effect should be significant. All core java.awt and java.swing references are now made from within org.jmol.awt or org.jmol.export (where all the file dialogs are). org.jmol.console, org.jmol.modelkit, and org.jmol.viewer.MouseManager14.java (now Mouse.java) have all been moved into org.jmol.awt. This is in preparation for Mario Kosmiskas integrating his Jmol Android and NET apps into core Jmol. Both Android and NET will be separate Java/C## projects (within the Jmol Sourceforge project) that link to the Jmol project, so developers not interested in those won't need the Android SDK. In addition, I've been working with Adam Williams at U-Mass Amherst on adding JSON-protocol NIO socket and kiosk capability to the Jmol app. What this means is that you will be able to start Jmol in kiosk mode, which basically makes the application look like the applet (an undecorated black square) that can be projected onto a wall. By specifying a port number on the Jmol command line, you will be able to communicate with Jmol via that port essentially like applets communicate with each other using SYNC commands. Adam has written a Kinect-driven host that takes this Jmol app as its client. Jmol listens asynchronously on the port for raw mouse motions, script commands, and SYNC messages using a simple JSON protocol, and reports back to the host when a script has completed. Adam has installed this at U-Mass Amherst as the Molecular Playground http
[Jmol-developers] serious refactoring of Jmol
Over the past few days I've been doing some major refactoring of Jmol 12. The changes should be transparent, but the overall effect should be significant. All core java.awt and java.swing references are now made from within org.jmol.awt or org.jmol.export (where all the file dialogs are). org.jmol.console, org.jmol.modelkit, and org.jmol.viewer.MouseManager14.java (now Mouse.java) have all been moved into org.jmol.awt. This is in preparation for Mario Kosmiskas integrating his Jmol Android and NET apps into core Jmol. Both Android and NET will be separate Java/C## projects (within the Jmol Sourceforge project) that link to the Jmol project, so developers not interested in those won't need the Android SDK. In addition, I've been working with Adam Williams at U-Mass Amherst on adding JSON-protocol NIO socket and kiosk capability to the Jmol app. What this means is that you will be able to start Jmol in kiosk mode, which basically makes the application look like the applet (an undecorated black square) that can be projected onto a wall. By specifying a port number on the Jmol command line, you will be able to communicate with Jmol via that port essentially like applets communicate with each other using SYNC commands. Adam has written a Kinect-driven host that takes this Jmol app as its client. Jmol listens asynchronously on the port for raw mouse motions, script commands, and SYNC messages using a simple JSON protocol, and reports back to the host when a script has completed. Adam has installed this at U-Mass Amherst as the Molecular Playground http://molecularPlayground.org and we are currently installing a version of this at St. Olaf. So maybe the theme for the week is from small to large -- Jmol on cell phones and in public spaces. Bob -- 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] serious refactoring of Jmol
This looks cool...I'm going to see if I can convince my School to set something up. Jonathan On Sep 27, 2011, at 10:55 AM, Robert Hanson wrote: Over the past few days I've been doing some major refactoring of Jmol 12. The changes should be transparent, but the overall effect should be significant. All core java.awt and java.swing references are now made from within org.jmol.awt or org.jmol.export (where all the file dialogs are). org.jmol.console, org.jmol.modelkit, and org.jmol.viewer.MouseManager14.java (now Mouse.java) have all been moved into org.jmol.awt. This is in preparation for Mario Kosmiskas integrating his Jmol Android and NET apps into core Jmol. Both Android and NET will be separate Java/C## projects (within the Jmol Sourceforge project) that link to the Jmol project, so developers not interested in those won't need the Android SDK. In addition, I've been working with Adam Williams at U-Mass Amherst on adding JSON-protocol NIO socket and kiosk capability to the Jmol app. What this means is that you will be able to start Jmol in kiosk mode, which basically makes the application look like the applet (an undecorated black square) that can be projected onto a wall. By specifying a port number on the Jmol command line, you will be able to communicate with Jmol via that port essentially like applets communicate with each other using SYNC commands. Adam has written a Kinect-driven host that takes this Jmol app as its client. Jmol listens asynchronously on the port for raw mouse motions, script commands, and SYNC messages using a simple JSON protocol, and reports back to the host when a script has completed. Adam has installed this at U-Mass Amherst as the Molecular Playground http://molecularPlayground.org and we are currently installing a version of this at St. Olaf. So maybe the theme for the week is from small to large -- Jmol on cell phones and in public spaces. Bob -- 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 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
