Re: [Jmol-developers] current work
Bob Hanson wrote. -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0: double bonds in the plane of the atoms, not twisty with orientation. I quite agree with Jonathan, I'm not sure I would like this default changed. Must play with it but haven't got the time now. -- smooth on-the-fly language switching Can you elaborate mre on what that means? We already could switch languages. Does it mean that the application reload is no longer done? -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] current work
2010/9/19 Angel Herráez angel.herr...@uah.es Bob Hanson wrote. -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0: double bonds in the plane of the atoms, not twisty with orientation. I quite agree with Jonathan, I'm not sure I would like this default changed. Must play with it but haven't got the time now. OK, that's probably enough to say we shouldn't change it. People who want this will need to enter: set multipleBondSpacing 0.35 set multipleBondRadiusFactor 0.7 if they want multiple bonds in-line. -- smooth on-the-fly language switching Can you elaborate mre on what that means? We already could switch languages. Does it mean that the application reload is no longer done? With the applet menu you don't notice it, but with the application Jmol was messing up menu and dialog items and was totally reloading the model. Now it just instantly changes the button and menu item names. Every single button, label, and menu item is simply switched over instantly. You can see it especially if you open the console with either the application or applet and type set language fr set language de set language en Bob -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] current work
On Wed, Sep 15, 2010 at 7:38 PM, Jonathan Gutow gu...@uwosh.edu wrote: On Sep 15, 2010, at 10:41 AM, Robert Hanson wrote: -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0: double bonds in the plane of the atoms, not twisty with orientation. This is the default I always expected, but the current default makes sure that you can tell which are double bonds. I'm not sure if I really want it changed to what I expected I believe that the original argument for doing it the current way is to ensure that the double bond always has full visibility... if in the atoms plane (which atoms), and that plane happens to be perpendicular to the eyes, then one will not see the double bond, but a single bond instead... Egon -- Dr E.L. Willighagen Post-doc @ Uppsala University (only until 2010-09-30) Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] current work/double bond view...
I've played with Bob's example and here is my opinion. Before I used Jmol I thought the default should be double bonds all in one plane, but now feel that Jmol's present default where you see the double bonds no matter what the viewing angle is better. I do think the scale of the double bond should be set smaller than the current default and like the idea of an option to make the double bond plane fixed relative to the molecule axes. The double bonds in a fixed plane should be an option not the default. Should we do a poll and maybe on the user's list? Joanthan 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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] current work
please play with it and see what you think. On Wed, Sep 15, 2010 at 12:38 PM, Jonathan Gutow gu...@uwosh.edu wrote: On Sep 15, 2010, at 10:41 AM, Robert Hanson wrote: -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0: double bonds in the plane of the atoms, not twisty with orientation. This is the default I always expected, but the current default makes sure that you can tell which are double bonds. I'm not sure if I really want it changed to what I expected double bond cylinders somewhat smaller than single bond cylinders this is very good. -- smooth on-the-fly language switching + 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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- 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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] current work
This week I'm working on a number of problems and have not uploaded my changes to 12.1 because I have several items that also need implementing in 12.0. Here's a short list: -- isosurface map MEP has completely rewritten code. We can now produce highly ACCURATE electrostatic maps for proteins given a decent set of partial charges. No need for huge map files. -- a variety of bugs relating to saving JVXL files for specialized surfaces (capped isosurfaces, for example) -- console code refactored to make it possible to embed either the applet or the application console in another applet or application -- multipleBondRadiusFactor and multipleBondSpacing options -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0: double bonds in the plane of the atoms, not twisty with orientation. double bond cylinders somewhat smaller than single bond cylinders -- smooth on-the-fly language switching 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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] current work
On Sep 15, 2010, at 10:41 AM, Robert Hanson wrote: -- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0: double bonds in the plane of the atoms, not twisty with orientation. This is the default I always expected, but the current default makes sure that you can tell which are double bonds. I'm not sure if I really want it changed to what I expected double bond cylinders somewhat smaller than single bond cylinders this is very good. -- smooth on-the-fly language switching + 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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
