Re: [Jmol-developers] [Jmol-users] Jmol 11.6 last days before release
[switching to jmol-developers list] Egon, Great. I just added support for Amber molecular dynamics file loading -- 1(topology file) + n(coordinate file) and with the FILTER option and a new option to allow selective first,last,step loading of coordinate trajectories, Jmol should be significantly useful in that area. That's in 11.7, not 11.6. First test is encouraging. Also, I spent the weekend writing an AVI video creator. I learned a lot, mostly how difficult it is to create real video animations. Alas, I can write AVI files, but the JPG files required for those are a special type that the JpgEncoder in Jmol doesn't write (at least by default). I'd try to fix that, but then I learned that Quicktime doesn't read AVI files of this sort, and there are other issues as well. Mostly I was just trying another angle. I've left the code in there commented out in case we ever revive that idea. I think I'll give up on the JPG -- MJPEG idea. It has no support in the video community, and apparently it was created ad hoc with no real specifications. Just a royal pain. Probably the only dependable way to do this is as an animated GIF. But then I have to figure out how to approximate the colors of Jmol within a 256-color set. No simple solution that I see for that. (Rolf, I haven't looked into http://www.imagemagick.org yet.) Question: Would people be interested in an animate GIF producer from spin, vibration, navigation, script, or (what else?) operations? Bob On Mon, Sep 29, 2008 at 5:42 AM, Egon Willighagen [EMAIL PROTECTED] wrote: On Sat, Sep 27, 2008 at 6:33 PM, Robert Hanson [EMAIL PROTECTED] wrote: I'm hoping we can release 11.6 Wednesday. Please finish all translations and notify me of bugs before then. Translated applet and app into NL. Quite a few textual changes... Egon -- http://chem-bla-ics.blogspot.com/ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list [EMAIL PROTECTED] 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] [Jmol-users] Jmol 11.6 last days before release
On Mon, Sep 29, 2008 at 3:42 PM, Robert Hanson [EMAIL PROTECTED] wrote: I just added support for Amber molecular dynamics file loading -- 1(topology file) + n(coordinate file) and with the FILTER option and a new option to allow selective first,last,step loading of coordinate trajectories, Jmol should be significantly useful in that area. That's in 11.7, not 11.6. First test is encouraging. That sounds great. I have to check with some FoldingAtHome projects since some are using an Amber core to do the molecular dynamics. I hope they are producing the correct files to view them in Jmol :) Nico - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] [Jmol-users] Jmol 11.6 last days before release
I just added support for Amber molecular dynamics file loading -- 1(topology file) + n(coordinate file) and with the FILTER option and a new option to allow selective first,last,step loading of coordinate trajectories, Jmol should be significantly useful in that area. That's in 11.7, not 11.6. First test is encouraging. I have a friend doing MD. I'll try and see if we can test some files. Question: Would people be interested in an animate GIF producer from spin, vibration, navigation, script, or (what else?) operations? I think so. It would be a nice addition, although of course it's better to convince people to just use Jmol. Regarding video formats, I think that MPEG would be a better choice, more cross-OS, particularly if AVI gives trouble. But I have no idea of the difficulties involved. Thanks for the efforts, Bob! - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] [Jmol-users] Jmol 11.6 last days before release
Robert Hanson wrote: [switching to jmol-developers list] Also, I spent the weekend writing an AVI video creator. I learned a lot, mostly how difficult it is to create real video animations. Alas, I can write AVI files, but the JPG files required for those are a special type that the JpgEncoder in Jmol doesn't write (at least by default). I'd try to fix that, but then I learned that Quicktime doesn't read AVI files of this sort, and there are other issues as well. Mostly I was just trying another angle. I've left the code in there commented out in case we ever revive that idea. I think I'll give up on the JPG -- MJPEG idea. It has no support in the video community, and apparently it was created ad hoc with no real specifications. Just a royal pain. MJPEG seems to be used very commonly by digital cameras. I didn't observe any problems yet with displaying MJPEG videos produced by my camera with several viewers including Windows media player, but I didn't try Quicktime yet. Probably the only dependable way to do this is as an animated GIF. But then I have to figure out how to approximate the colors of Jmol within a 256-color set. No simple solution that I see for that. (Rolf, I haven't looked into http://www.imagemagick.org yet.) Question: Would people be interested in an animate GIF producer from spin, vibration, navigation, script, or (what else?) operations? I might be interested because we are currently thinking about exporting animated views from Jmol. (But it's just brainstorming to develop new ideas for the JenaLib.) Regards, Rolf - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] [Jmol-users] Jmol 11.6 last days before release
On Sep 29, 2008, at 8:42 AM, Robert Hanson wrote: Probably the only dependable way to do this is as an animated GIF. But then I have to figure out how to approximate the colors of Jmol within a 256-color set. No simple solution that I see for that. (Rolf, I haven't looked into http://www.imagemagick.org yet.) I used imagemagick a couple of times to produce animated gifs from Jmol. The issue is that the files have a tendency to be very big if the resolution is reasonable. It seems much more efficient to use the combination of Jmol + data file + script. The only issue being that the user has to have a JVM. My two cents. Jonathan Dr. Jonathan H. Gutow Chemistry Department [EMAIL PROTECTED] UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/faculty_staff/gutow/ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] [Jmol-users] Jmol 11.6 last days before release
OK, so it might be worthwhile to check out some more files like this. Rolf, can you send me some example M-JPEG files that work for you. I'm willing to give it one more shot. Bob On Mon, Sep 29, 2008 at 10:37 AM, Rolf Huehne [EMAIL PROTECTED]wrote: Robert Hanson wrote: [switching to jmol-developers list] Also, I spent the weekend writing an AVI video creator. I learned a lot, mostly how difficult it is to create real video animations. Alas, I can write AVI files, but the JPG files required for those are a special type that the JpgEncoder in Jmol doesn't write (at least by default). I'd try to fix that, but then I learned that Quicktime doesn't read AVI files of this sort, and there are other issues as well. Mostly I was just trying another angle. I've left the code in there commented out in case we ever revive that idea. I think I'll give up on the JPG -- MJPEG idea. It has no support in the video community, and apparently it was created ad hoc with no real specifications. Just a royal pain. MJPEG seems to be used very commonly by digital cameras. I didn't observe any problems yet with displaying MJPEG videos produced by my camera with several viewers including Windows media player, but I didn't try Quicktime yet. Probably the only dependable way to do this is as an animated GIF. But then I have to figure out how to approximate the colors of Jmol within a 256-color set. No simple solution that I see for that. (Rolf, I haven't looked into http://www.imagemagick.org yet.) Question: Would people be interested in an animate GIF producer from spin, vibration, navigation, script, or (what else?) operations? I might be interested because we are currently thinking about exporting animated views from Jmol. (But it's just brainstorming to develop new ideas for the JenaLib.) Regards, Rolf - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ 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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
