Re: [Jmol-developers] page needs updating
The Jmol website should now be up to date :) On Thu, Oct 9, 2008 at 12:38 PM, Angel Herráez [EMAIL PROTECTED] wrote: I have commited the update to display 11.6 as current version nr. in the front page and the update of the applet files for the website. I want to check that the examples/demos work well, but I cannot do that right now locally due to the applet path, so I'll test them once the changes are in the website. (I tried to mock it by replacing the applet in /jmol/ with the signed applet files, but Jmol in the front page didn't finish loading) - 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] page needs updating
On Sat, Oct 11, 2008 at 12:57 PM, Nicolas Vervelle [EMAIL PROTECTED]wrote: The Jmol website should now be up to date :) Really strange : I got security exceptions on the first attempt to view pages, but now it seems ok. 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] page needs updating
On 11 Oct 2008 at 13:14, Nicolas Vervelle wrote: Really strange : I got security exceptions on the first attempt to view pages, but now it seems ok. I've had no trouble. I'm checking the demo pages and while testing them locally I had some trouble convincing the browser to use the new applet - it insisted on loading 11.4.6 from the Java cache. Everything seems to be working I noticed today some significant delay between Jmol's black panel loaded and the loading of the promotion model. This may confuse users, so I'm adding a note to the script, saying Jmol has finished loading | Now loading content... Nico, Egon, are these phrases OK? Jmol a fini de télécharger | Maintenant téléchargement du contenu... Jmol heeft het downladen gebeëindigd | Nu downloadend inhoud... - 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] page needs updating
On Sat, Oct 11, 2008 at 2:38 PM, Angel Herráez [EMAIL PROTECTED] wrote: Nico, Egon, are these phrases OK? Jmol a fini de télécharger | Maintenant téléchargement du contenu... I would rather have something like : Téléchargement de Jmol terminé | Téléchargement du contenu en cours... 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] MD trajectories for 11.7
Matt, I did check this out more carefully, and I see now that there was a
bug in Jmol for appended trajectories. It's fixed, but it's in Jmol 11.7.3,
which has not been released yet. If you are interested in getting a look at
this, take a look at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=1
JAR files for 11.7.3 are in
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Bob
On Thu, Oct 9, 2008 at 10:09 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Hey, Matt, you might be in luck.
On Thu, Oct 9, 2008 at 2:01 PM, Matthew Zwier [EMAIL PROTECTED] wrote:
At least, I think you can Supposed to be able to. You are just
limited
to one trajectory step from EACH sequence loaded. I can't imagine why
that
would take any major amount of time if they are trajectories.
Yeah, as I said above, they're loaded as independent models, not
trajectories. It gets slow when the total number of atoms gets large,
as I suppose one would expect if there's a loop over all 40,000 atoms
occurring each animation frame.
I'm happy to do the coding if anything is necessary there. Doesn't sound
too
involved to me. Keep talking
Sounds like the machinery is there already, and that I just haven't
kept up with recent development enough to know. Loading each run as a
trajectory should do it.
Right. It's all there. You can't use both the append and the trajectory
keywords at the same time right now, but in this case you don't need the
trajectory keyword, so you can do:
load files u.mdtop FILTER ![WAT],![URE] COORD {0 -1 5}
mdcrd::prod1.mdcrd mdcrd::prod2.mdcrd
load append u.mdtop FILTER ![WAT],![URE] COORD {0 -1 5}
mdcrd::prod3.mdcrd mdcrd::prod4.mdcrd
frame *;
display 1.1,2.1
delay 0.1
display 1.2,2.2
delay 0.1
display 1.3,2.3
delay 0.1
...
or if you wanted an animation, something like
var nSec = 0.1
for (var i = 1; i 10;i = i + 1)
script inline @{display 1. + i + , 2. + i}
delay @nSec
end for
I tried this on a simple model (7700 atoms), and it went very smoothly.
Note that if you add a write command (and you are using the Jmol
application), then you can make a movie of the overlaid trajectories:
for (var i = 1; i 10;i = i + 1)
script inline @{display 1. + i + , 2. + i}
write image 500 500 @{movie + ( + i)[-3][0] + .jpg}
end for
And then use some other software to combine those JPEG stills into an AVI
file.
I do use per-frame transparency, which would break if
color/transparency information is logically tied to the topology
rather than the coordinates (the latter being what changes on a
per-animation-frame basis). If there could be per-trajectory-frame
color attributes, it'd be a pretty big help. The only other helpful
thing would be more than 8 levels of transparency (though I can't
imagine more than 20 would matter).
All you do is make a for/end for loop as above and basically design your
own animation.
Eventually, my dream is to produce animations not only of the atoms
but also of molecular orbitals, but I strongly suspect that's too
computationally- or memory-intensive to do in an interactive
environment.
Nah. Actually, you could do this. It would require some initial set up.
I wonder how slow it would be:
1) set up your trajectory data.
2) create the molecular orbitals using Gaussian in terms of a CUBE file for
each stage along the way.
3) use Jmol or Jvxl.jar to create JVXL files (200:1 compressed surfaces) of
those orbitals from the CUBE files.
That's the slow part. Now load the trajectory data, and as above drive the
animation, but this time include an isosurface command that loads the
desired surface from the JVXL files.
If these are reasonably small molecules, I'll bet the JVXL file will load
and display almost instantly.
Might work.
Bob
Thanks for the reply and discussion!
Cheers,
Matt Z.
-
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
--
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
[Jmol-developers] Is script checking still working ?
Hi, Script checking seems very slow with the latest versions (as if it was not only checking the script, but also running it). Something has changed ? 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] Is script checking still working ?
The -c flag checks scripts, but it also does all the file opening, and that will take time. To check a script without file loading, you need to create a little script that contains: script xxx.spt check noload and then use Jmol -s thatscript.spt Bob On Sat, Oct 11, 2008 at 4:44 PM, Robert Hanson [EMAIL PROTECTED] wrote: I don't think so. I'll check. I usually do the script running, not just checking, so we'll see. On Sat, Oct 11, 2008 at 4:22 PM, Nicolas Vervelle [EMAIL PROTECTED]wrote: Hi, Script checking seems very slow with the latest versions (as if it was not only checking the script, but also running it). Something has changed ? 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 -- 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 -- 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] Is script checking still working ?
I don't think so. I'll check. I usually do the script running, not just checking, so we'll see. On Sat, Oct 11, 2008 at 4:22 PM, Nicolas Vervelle [EMAIL PROTECTED]wrote: Hi, Script checking seems very slow with the latest versions (as if it was not only checking the script, but also running it). Something has changed ? 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 -- 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
[Jmol-developers] [ jmol-Feature Requests-1836521 ] multiple scripts per command-line
Feature Requests item #1836521, was opened at 2007-11-22 09:27 Message generated for change (Settings changed) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detailatid=379136aid=1836521group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Interface Improvements Group: None Status: Closed Priority: 5 Private: No Submitted By: Rolf Huehne (rhuehne) Assigned to: Bob Hanson (hansonr) Summary: multiple scripts per command-line Initial Comment: Currently (Jmol 11.3.44) only the first -s option provided in the command-line is used. Additional ones are ignored. It would be very helpful (e.g.: for batch image generation) to be able to execute several scripts provided per command-line option. (This would avoid for example the error-prone need for several almost identical complex scripts.) If this is not possible (or even then?) it would also help to be able to set one (or several?) Jmol variables with a command-line option. Or alternatively having access to environment variables within Jmol scripting. -- Comment By: Bob Hanson (hansonr) Date: 2008-10-11 21:22 Message: new feature for Jmol 11.7.3: jmol --jmolscript some script here jmol -j some script here jmol -j echo \testing here\ of course, this script could call other scripts: jmol -j script somefile1.spt;script somefile2.spt;script somefile3.spt or jmol -j script somefile1.spt check noload -- You can respond by visiting: https://sourceforge.net/tracker/?func=detailatid=379136aid=1836521group_id=23629 - 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
[Jmol-developers] Application: Gaussian Dialog
Jmol Developers, I finally got around to adding Andy Turner's Gaussian Input dialog -- it's very nice. It's under File...Export Checked in as part of 11.7.3 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 - 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] Application: Gaussian Dialog
Jmol Developers, I finally got around to adding Andy Turner's Gaussian Input dialog -- it's very nice. It's under File...Export Checked in as part of 11.7.3 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 - 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
