Re: [Jmol-users] a related popup window question....
Thanks Angel -- Yes, it definitely turned out to be a memory issue. My inexperience is another! I was stumped since the Jmol graphic stopped responding, but Jmol itself was still running and doing stuff -- I could still enter commands into the console and get appropriate responses. Now I know that that is a hallmark of Java exceptions, including out-of-memory errors. With regard to large windows and the memory issue, I've settled here on creating a pop-up window that is large enough for end-users to have a big view but which is fixed in size so that I know that it won't immediately eat up all of the memory. I've given up the ability for them to re-size, but it seems a reasonable trade-off. Thanks very much, Tom On Thu, Aug 28, 2008 at 11:13 AM, Angel Herráez [EMAIL PROTECTED]wrote: Hi Tom I'm probably late in joining this thread, but since there has been no final comment, here's my 2 cents 1) Your problem looks to me as more related to a specific browser and JVM that to Jmol version (but I may be wrong). Of course, memory is an issue. 2) i) be able to stipulate the size of the popup Applet and have it be a fixed size, or You can always specify a fixed size applet; if the user maximizes the window, he will see blank space around the applet. (But it's great to be able to increase the applet size at will; maybe you could include a warning in yor pop-up window; after all, the memory allocated to Java is an user option. To the point: jmolApplet(600,script javascript:getState()) will give you a fixed size, 600 pixels, square applet. 3) is there a means of specifying the size of the popup window and not allowing it to be resized once created?? Certainly! Say you are using woptions=menubar=yes,resizable=1,scrollbars,alwaysRaised,width=600,height=600,left=50 newwin=open(JmolPopup.htm,jmol_+sm,woptions) Then, change to woptions=menubar=yes,resizable=0,scrollbars,alwaysRaised,width=600,height=600,left=50 4) ii) your idea, to have an upper limit on how big it can get. I find this very tricky to implement, if even possible. 5) Curiously, the popup window is more resistant to this blanking effect using MS IExplorer than with Firefox (3.0.1). In my experience, Firefox (2.0) implementation of JVM (1.5 - 1.6) is much more unstable than IE's - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
I've gone ahead and added for Jmol 11.6.RC12 the applet param tag
maximumSize. This can be set to a maximum size for which the height and
width are not allowed to exceed when resizing. I think this will be a more
user-friendly option. The way to invoke it would be
jmolInitialize(...)
jmolSetCallback(maximumSize, 400)
jmolApplet()
It may seem odd to set this using jmolSetCallback(), but jmolSetCallback is
really just a general jmolSetParameter function. I suppose we should add
to Jmol.js
function jmolSetParameter(param, value) {
jmolSetCallback(param, value)
}
So that's clearer.
I didn't make it settable via a script command because it seems to me more
an aspect of building the applet that the developer might set rather than
something that the user should be able to set on the fly.
Bob
On Fri, Aug 29, 2008 at 12:30 PM, Thomas Stout [EMAIL PROTECTED]wrote:
Thanks Angel --
Yes, it definitely turned out to be a memory issue. My inexperience is
another! I was stumped since the Jmol graphic stopped responding, but Jmol
itself was still running and doing stuff -- I could still enter commands
into the console and get appropriate responses. Now I know that that is a
hallmark of Java exceptions, including out-of-memory errors.
With regard to large windows and the memory issue, I've settled here on
creating a pop-up window that is large enough for end-users to have a big
view but which is fixed in size so that I know that it won't immediately
eat up all of the memory. I've given up the ability for them to re-size,
but it seems a reasonable trade-off.
Thanks very much,
Tom
On Thu, Aug 28, 2008 at 11:13 AM, Angel Herráez [EMAIL PROTECTED]wrote:
Hi Tom
I'm probably late in joining this thread, but since there has been no
final comment, here's
my 2 cents
1)
Your problem looks to me as more related to a specific browser and JVM
that to Jmol
version (but I may be wrong). Of course, memory is an issue.
2)
i) be able to stipulate the size of the popup Applet and have it be a
fixed size, or
You can always specify a fixed size applet; if the user maximizes the
window, he will see
blank space around the applet. (But it's great to be able to increase the
applet size at will;
maybe you could include a warning in yor pop-up window; after all, the
memory allocated to
Java is an user option.
To the point:
jmolApplet(600,script javascript:getState())
will give you a fixed size, 600 pixels, square applet.
3)
is there a means of specifying the size of the popup window and not
allowing it to be
resized once created??
Certainly!
Say you are using
woptions=menubar=yes,resizable=1,scrollbars,alwaysRaised,width=600,height=600,left=50
newwin=open(JmolPopup.htm,jmol_+sm,woptions)
Then, change to
woptions=menubar=yes,resizable=0,scrollbars,alwaysRaised,width=600,height=600,left=50
4)
ii) your idea, to have an upper limit on how big it can get.
I find this very tricky to implement, if even possible.
5)
Curiously, the popup window is more resistant to this blanking effect
using MS IExplorer
than with Firefox (3.0.1).
In my experience, Firefox (2.0) implementation of JVM (1.5 - 1.6) is much
more unstable
than IE's
-
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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Grand prize is a trip for two to an Open Source event anywhere in the world
Re: [Jmol-users] a related popup window question....
Rolf Huehne wrote: Thomas Stout wrote: Thanks Angel -- Yes, it definitely turned out to be a memory issue. My inexperience is another! I was stumped since the Jmol graphic stopped responding, but Jmol itself was still running and doing stuff -- I could still enter commands into the console and get appropriate responses. Now I know that that is a hallmark of Java exceptions, including out-of-memory errors. With regard to large windows and the memory issue, I've settled here on creating a pop-up window that is large enough for end-users to have a big view but which is fixed in size so that I know that it won't immediately eat up all of the memory. I've given up the ability for them to re-size, but it seems a reasonable trade-off. Instead of providing an automatic resize function you could provide a manual resize option using input fields. This way you could easily set a maximum size limit by your Javascript code that does the actual resizing. You wouldn't even need input fields. You could tie for example the 'body' tag with the 'onResize' event to a Javascript function that resizes the applet with an upper limit. I just did a similar thing (with a lower limit) a few days ago for our PDB file viewer: http://www.fli-leibniz.de/cgi-bin/idb_send-rh.pl?CODE=1dehMIME=html 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
Thomas Stout wrote: Thanks Angel -- Yes, it definitely turned out to be a memory issue. My inexperience is another! I was stumped since the Jmol graphic stopped responding, but Jmol itself was still running and doing stuff -- I could still enter commands into the console and get appropriate responses. Now I know that that is a hallmark of Java exceptions, including out-of-memory errors. With regard to large windows and the memory issue, I've settled here on creating a pop-up window that is large enough for end-users to have a big view but which is fixed in size so that I know that it won't immediately eat up all of the memory. I've given up the ability for them to re-size, but it seems a reasonable trade-off. Instead of providing an automatic resize function you could provide a manual resize option using input fields. This way you could easily set a maximum size limit by your Javascript code that does the actual resizing. 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
Hi Tom I'm probably late in joining this thread, but since there has been no final comment, here's my 2 cents 1) Your problem looks to me as more related to a specific browser and JVM that to Jmol version (but I may be wrong). Of course, memory is an issue. 2) i) be able to stipulate the size of the popup Applet and have it be a fixed size, or You can always specify a fixed size applet; if the user maximizes the window, he will see blank space around the applet. (But it's great to be able to increase the applet size at will; maybe you could include a warning in yor pop-up window; after all, the memory allocated to Java is an user option. To the point: jmolApplet(600,script javascript:getState()) will give you a fixed size, 600 pixels, square applet. 3) is there a means of specifying the size of the popup window and not allowing it to be resized once created?? Certainly! Say you are using woptions=menubar=yes,resizable=1,scrollbars,alwaysRaised,width=600,height=600,left=50 newwin=open(JmolPopup.htm,jmol_+sm,woptions) Then, change to woptions=menubar=yes,resizable=0,scrollbars,alwaysRaised,width=600,height=600,left=50 4) ii) your idea, to have an upper limit on how big it can get. I find this very tricky to implement, if even possible. 5) Curiously, the popup window is more resistant to this blanking effect using MS IExplorer than with Firefox (3.0.1). In my experience, Firefox (2.0) implementation of JVM (1.5 - 1.6) is much more unstable than IE's - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
You have total control over the popup characteristics -- it's your page! The only reason it's resizing is that you have percentages listed in the jmolApplet command, I think. Bob On Wed, Aug 20, 2008 at 4:30 PM, Thomas Stout [EMAIL PROTECTED]wrote: Yes: I've seen the users make the windows pretty big (especially when they hit the maximize window button in the upper right of the browser window -- the window then becomes as large as the monitor some of those are in the 2000 pixels dimensions now). I'd be interested in two possible solutions: i) be able to stipulate the size of the popup Applet and have it be a fixed size, or ii) your idea, to have an upper limit on how big it can get. Both have advantages: the fixed size popup Applet lets me have more control over layout and design, but the upper size limit is certainly much more flexible for the end user. -Tom On Wed, Aug 20, 2008 at 2:22 PM, Robert Hanson [EMAIL PROTECTED] wrote: There's your answer. Out of memory. How big are these resizes? height/width? I wonder if a settable maximumWindowSize option might be in order here. Bob On Wed, Aug 20, 2008 at 3:00 PM, Thomas Stout [EMAIL PROTECTED]wrote: Exception in thread AWT-EventQueue-3 java.lang.OutOfMemoryError: Java heap space at org.jmol.g3d.Platform3D.allocateTBuffers(Platform3D.java:89) I see this behavior on both both WinXP and linux (CentOS) and both a pretty hefty machines (graphics and RAM-wise) -Tom On 8/20/08, Robert Hanson [EMAIL PROTECTED] wrote: ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED] wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.Net email is sponsored by the Moblin
[Jmol-users] a related popup window question....
It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom Title: Jmol Popup Model Refresh model Note - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
Thomas Stout wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? It sounds similar to a problem that I occasionally observed when I developed the manual resize function for our 'JenaLib Jmol Viewer'. My workaround is to initially open the applet with a slightly larger size (602x602 pixel) and then adjust the size to the final value by the following commands: document.getElementById(jmolApplet0).style.width = 600; document.getElementById(jmolApplet0).style.height = 600; This still seems to work with Jmol 11.6.RC8. You can try it at this URL: http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=2arcJMOLVERSION=11.6.RC8 But I never tried automatical adjustment because it is not suitable for our interface. 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
Hmmm - thanks Rolf. It sounds like it would be best to avoid the end-user arbitrarily resizing the popup window to make it larger/smaller My beta-test users are all trying to make the popup window larger by dragging the browser window (or using the maximize button in the upper right window bar) -- is there a means of specifying the size of the *popup* window and not allowing it to be resized once created?? -Tom On Wed, Aug 20, 2008 at 10:49 AM, Rolf Huehne [EMAIL PROTECTED]wrote: Thomas Stout wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? It sounds similar to a problem that I occasionally observed when I developed the manual resize function for our 'JenaLib Jmol Viewer'. My workaround is to initially open the applet with a slightly larger size (602x602 pixel) and then adjust the size to the final value by the following commands: document.getElementById(jmolApplet0).style.width = 600; document.getElementById(jmolApplet0).style.height = 600; This still seems to work with Jmol 11.6.RC8. You can try it at this URL: http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=2arcJMOLVERSION=11.6.RC8 But I never tried automatical adjustment because it is not suitable for our interface. 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED]wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
Yes, the display fails just on re-sizing the window (no model manipulation). Without re-sizing the window, one can manipulate the model and do anything one wishes with Jmol with complete stability. Curiously, the popup window is more resistant to this blanking effect using MS IExplorer than with Firefox (3.0.1). Attempting IEtabs in Firefox completely locks up Firefox and is a Bad Thing! I was able to get the blanking to occur on about the 4th ot 5th re-sizing (of the same popup window) and it did throw a Java exception that looks like an our of memory issue: Exception in thread AWT-EventQueue-3 java.lang.OutOfMemoryError: Java heap space at org.jmol.g3d.Platform3D.allocateTBuffers(Platform3D.java:89) at org.jmol.g3d.Graphics3D.setPass2(Graphics3D.java:371) at org.jmol.viewer.Viewer.render(Viewer.java:3204) at org.jmol.viewer.Viewer.getImage(Viewer.java:3194) at org.jmol.viewer.Viewer.renderScreenImage(Viewer.java:3180) at org.jmol.applet.Jmol.update(Jmol.java:562) at org.jmol.applet.Jmol.paint(Jmol.java:528) at org.jmol.appletwrapper.AppletWrapper.paint(AppletWrapper.java:178) at sun.awt.RepaintArea.paintComponent(Unknown Source) at sun.awt.RepaintArea.paint(Unknown Source) at sun.awt.windows.WComponentPeer.handleEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) I see this behavior on both both WinXP and linux (CentOS) and both a pretty hefty machines (graphics and RAM-wise) -Tom On 8/20/08, Robert Hanson [EMAIL PROTECTED] wrote: ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED]wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
I've confirmed the out-of-memory issue. Adding -Xm256M into my Java control panel (found this info on the Jmol wiki: http://wiki.jmol.org/index.php/Jmol_Applet) seems to eliminate the problem BTW, does anyone know how to achieve this for a browser running on linux? Cheers, Tom On Wed, Aug 20, 2008 at 1:00 PM, Thomas Stout [EMAIL PROTECTED]wrote: Yes, the display fails just on re-sizing the window (no model manipulation). Without re-sizing the window, one can manipulate the model and do anything one wishes with Jmol with complete stability. Curiously, the popup window is more resistant to this blanking effect using MS IExplorer than with Firefox (3.0.1). Attempting IEtabs in Firefox completely locks up Firefox and is a Bad Thing! I was able to get the blanking to occur on about the 4th ot 5th re-sizing (of the same popup window) and it did throw a Java exception that looks like an our of memory issue: Exception in thread AWT-EventQueue-3 java.lang.OutOfMemoryError: Java heap space at org.jmol.g3d.Platform3D.allocateTBuffers(Platform3D.java:89) at org.jmol.g3d.Graphics3D.setPass2(Graphics3D.java:371) at org.jmol.viewer.Viewer.render(Viewer.java:3204) at org.jmol.viewer.Viewer.getImage(Viewer.java:3194) at org.jmol.viewer.Viewer.renderScreenImage(Viewer.java:3180) at org.jmol.applet.Jmol.update(Jmol.java:562) at org.jmol.applet.Jmol.paint(Jmol.java:528) at org.jmol.appletwrapper.AppletWrapper.paint(AppletWrapper.java:178) at sun.awt.RepaintArea.paintComponent(Unknown Source) at sun.awt.RepaintArea.paint(Unknown Source) at sun.awt.windows.WComponentPeer.handleEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) I see this behavior on both both WinXP and linux (CentOS) and both a pretty hefty machines (graphics and RAM-wise) -Tom On 8/20/08, Robert Hanson [EMAIL PROTECTED] wrote: ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED]wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
There's your answer. Out of memory. How big are these resizes? height/width? I wonder if a settable maximumWindowSize option might be in order here. Bob On Wed, Aug 20, 2008 at 3:00 PM, Thomas Stout [EMAIL PROTECTED]wrote: Exception in thread AWT-EventQueue-3 java.lang.OutOfMemoryError: Java heap space at org.jmol.g3d.Platform3D.allocateTBuffers(Platform3D.java:89) I see this behavior on both both WinXP and linux (CentOS) and both a pretty hefty machines (graphics and RAM-wise) -Tom On 8/20/08, Robert Hanson [EMAIL PROTECTED] wrote: ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED]wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a related popup window question....
Yes: I've seen the users make the windows pretty big (especially when they hit the maximize window button in the upper right of the browser window -- the window then becomes as large as the monitor some of those are in the 2000 pixels dimensions now). I'd be interested in two possible solutions: i) be able to stipulate the size of the popup Applet and have it be a fixed size, or ii) your idea, to have an upper limit on how big it can get. Both have advantages: the fixed size popup Applet lets me have more control over layout and design, but the upper size limit is certainly much more flexible for the end user. -Tom On Wed, Aug 20, 2008 at 2:22 PM, Robert Hanson [EMAIL PROTECTED] wrote: There's your answer. Out of memory. How big are these resizes? height/width? I wonder if a settable maximumWindowSize option might be in order here. Bob On Wed, Aug 20, 2008 at 3:00 PM, Thomas Stout [EMAIL PROTECTED]wrote: Exception in thread AWT-EventQueue-3 java.lang.OutOfMemoryError: Java heap space at org.jmol.g3d.Platform3D.allocateTBuffers(Platform3D.java:89) I see this behavior on both both WinXP and linux (CentOS) and both a pretty hefty machines (graphics and RAM-wise) -Tom On 8/20/08, Robert Hanson [EMAIL PROTECTED] wrote: ever? even if you don't manipulate the model? Please check for Java console errors. On Wed, Aug 20, 2008 at 12:29 PM, Thomas Stout [EMAIL PROTECTED]wrote: It's odd that the question about syncing with pop-up applet windows came up today just as I noticed the following: with the applet (version 11.6RC7) creating pop-up windows with the contents of an applet in a web page works just fine, but when re-sizing that pop-up window, the structure disappears and does not refresh. I'm using JmolPopup.htm (attached). Does this occur for anyone else too, or is it just my implementation? Thanks, Tom - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - 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
