[Jmol-users] problem with pop-up in Java 6u10
Dear Jmol users: -- For your information -- I have found a Java bug repainting Jmol's pop-up menu when the latest Java (6u10) is installed. It seems to be related to the display driver/graphics card. I see it in Windows XP with any browser, only in my notebook but not in my desktop PC. It is absent in 6u7. It affects both applet and application (as well as other non-Jmol app applets like JChemPaint). I've reported it to Sun Java and it is described here: http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6773336 They shall be working on it. If you have a similar problem (the pop-up menu has white patches while you hover the mouse pointer over it), you may want to follow that bug tracking or even to report details about your system. Some screenshots are available at http://www31.websamba.com/jpeg62/javaproblem/ - 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] script to move echo
I can see you are having great fun, Frieda,
function moveEcho
for ( var i=0; i250; i = i + 2 )
x = i
y = 450 - i
set echo myecho @x @y
delay 0.1
end for
end function
On Wed, Nov 19, 2008 at 6:26 PM, Frieda Reichsman [EMAIL PROTECTED] wrote:
How would I then see the calculated values for x and y coordinates? Jmol's
output does not show the result of the calculations.
On Nov 19, 2008, at 4:01 PM, Robert Hanson wrote:
function moveEcho
for ( var i=0; i250; i = i + 2 )
set echo myecho @i @{450-i}
delay 0.1
end for
end function
On Wed, Nov 19, 2008 at 2:52 PM, Frieda Reichsman [EMAIL PROTECTED]wrote:
Hi,
I am trying to move an echo diagonally across the Jmol applet using a
function (I have created and positioned the echo at (0, 450) before
calling the function). I want the echo to stop at (250, 200) or
thereabouts.
function moveEcho
for ( var i=0; i250; i = i + 2 )
x = script(set echo myecho i + (450 - i) + ; delay 0.1;)
end for
end function
But I am getting a NaN for the second parameter, the y coord - here's
what Jmol says back to me:
for ( var i=0; i250; i = i + 2 )
x = script(set echo myecho + i + + 450-i ; delay 0.1;)
javascript: NaN set echo myecho 36 450
end for
(Note the NaN infront of set on the third line). So clearly Jmol
does not want to subtract i from 450. Am I not allowed to use the
variable twice in the same statement? Or am I missing something obvious?
Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742
Mon/Fri: 413-253-2405
Tu/Wed/Thu: 978-405-3228
mobile: 413-320-7449
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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
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--
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
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[Jmol-users] draw cylinder
On Nov 20, 2008, at 9:27 AM, Robert Hanson wrote:
I can see you are having great fun, Frieda,
Yes, I sure am! Hope to have something to show for it soon.
Meanwhile, I am trying to draw a cylinder with the following command:
draw cylinder diameter 45.0 {atomno=3198 and (nitrogen or oxygen)}
The result is a sphere. I realize I need to add a height parameter, of
some kind, to get a cylinder but I can't seem to figure out which
parameter it is in the documentation...
Also, just curious, could I get the diameter to be in Angstroms
instead of pixels?
-Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742
Mon/Fri: 413-253-2405
Tu/Wed/Thu: 978-405-3228
mobile: 413-320-7449
-
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Build the coolest Linux based applications with Moblin SDK win great prizes
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Re: [Jmol-users] draw cylinder
Frieda Reichsman wrote:
On Nov 20, 2008, at 9:27 AM, Robert Hanson wrote:
I can see you are having great fun, Frieda,
Yes, I sure am! Hope to have something to show for it soon.
Meanwhile, I am trying to draw a cylinder with the following command:
draw cylinder diameter 45.0 {atomno=3198 and (nitrogen or oxygen)}
The result is a sphere. I realize I need to add a height parameter, of
some kind, to get a cylinder but I can't seem to figure out which
parameter it is in the documentation...
I think it is similar as for a line. You will need 2 points that are the
center of the 2 circles that build the cylinder. It should be something
like:
draw cylinder diameter 45.0 {atomno=3198} {atomno=3199}
Also, just curious, could I get the diameter to be in Angstroms
instead of pixels?
I think that the decimal value that you use is already in Angstrom
because it is scaled with zoom.
Regards,
Rolf
-
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Re: [Jmol-users] script to move echo
On Wed, Nov 19, 2008 at 6:26 PM, Frieda Reichsman wrote: How would I then see the calculated values for x and y coordinates? Jmol's output does not show the result of the calculations. On Nov 20, 2008, at 9:27 AM, Robert Hanson wrote: function moveEcho for ( var i=0; i250; i = i + 2 ) x = i y = 450 - i set echo myecho @x @y delay 0.1 end for end function Using the above, I do not see the calculated values in the Jmol console... I get the following output in the console (repeated of course): for ( var i=0; i250; i = i + 2 ) x = i y = 450 - i set echo myecho @x @y delay 0.1 end for Also, the movement of the echo slows greatly when an isosurface is present. Is this a bug, or an inevitability? Frieda - 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] script to move echo
Frieda Reichsman wrote: On Wed, Nov 19, 2008 at 6:26 PM, Frieda Reichsman wrote: How would I then see the calculated values for x and y coordinates? Jmol's output does not show the result of the calculations. On Nov 20, 2008, at 9:27 AM, Robert Hanson wrote: function moveEcho for ( var i=0; i250; i = i + 2 ) x = i y = 450 - i set echo myecho @x @y delay 0.1 end for end function Using the above, I do not see the calculated values in the Jmol console... I get the following output in the console (repeated of course): If you want to see the values, add a print command within your loop: print x= + x + y= + y; 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] draw cylinder
Works - fantastic! Thanks.
On Nov 20, 2008, at 11:21 AM, Rolf Huehne wrote:
Frieda Reichsman wrote:
On Nov 20, 2008, at 9:27 AM, Robert Hanson wrote:
I can see you are having great fun, Frieda,
Yes, I sure am! Hope to have something to show for it soon.
Meanwhile, I am trying to draw a cylinder with the following command:
draw cylinder diameter 45.0 {atomno=3198 and (nitrogen or oxygen)}
The result is a sphere. I realize I need to add a height parameter,
of
some kind, to get a cylinder but I can't seem to figure out which
parameter it is in the documentation...
I think it is similar as for a line. You will need 2 points that are
the
center of the 2 circles that build the cylinder. It should be
something
like:
draw cylinder diameter 45.0 {atomno=3198} {atomno=3199}
Also, just curious, could I get the diameter to be in Angstroms
instead of pixels?
I think that the decimal value that you use is already in Angstrom
because it is scaled with zoom.
Regards,
Rolf
-
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challenge
Build the coolest Linux based applications with Moblin SDK win
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the world
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Re: [Jmol-users] draw cylinder
what you need are two ends, not one.
On Thu, Nov 20, 2008 at 10:04 AM, Frieda Reichsman [EMAIL PROTECTED]wrote:
On Nov 20, 2008, at 9:27 AM, Robert Hanson wrote:
I can see you are having great fun, Frieda,
Yes, I sure am! Hope to have something to show for it soon.
Meanwhile, I am trying to draw a cylinder with the following command:
draw cylinder diameter 45.0 {atomno=3198 and (nitrogen or oxygen)}
The result is a sphere. I realize I need to add a height parameter, of
some kind, to get a cylinder but I can't seem to figure out which
parameter it is in the documentation...
Also, just curious, could I get the diameter to be in Angstroms
instead of pixels?
-Frieda
-
Frieda Reichsman, PhD
Senior Research Scientist
The Concord Consortium
http://concord.org
25 Love Lane
Concord, MA 01742
Mon/Fri: 413-253-2405
Tu/Wed/Thu: 978-405-3228
mobile: 413-320-7449
-
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
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--
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
-
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Re: [Jmol-users] stateinfo and transparency of mep
Thanks for the fix Bob! Now (revision 10348) the stateinfo contains the transparency but I can see that the VDW surface has some colorless spots. Would it be possible to fix that? Thanks again Xavier On Wed, Nov 19, 2008 at 5:23 PM, Robert Hanson [EMAIL PROTECTED] wrote: it's a bug. I'll fix it tonight. On Wed, Nov 19, 2008 at 2:24 PM, Xavier Prat-Resina [EMAIL PROTECTED]wrote: Dear jmol users, I'm trying to open a new jmol window copying the old state using stateinfo. Everything works fine with only one exception: the transparency of a solvent mep isosurface. Here's an example: http://144.92.39.89/~xavier/web/openstate/http://144.92.39.89/%7Exavier/web/openstate/ when I click on the new window the state has no information about the transparency and the isosurface is opaque. I might be doing something wrong but I can't figure out what. By the way, if you try this with Mac/Firefox it doesn't work. There appear some NaN numbers in _setModelState that make the whole script fail. Has anyone seen something like that before? Thanks! Xavier -- Xavier Prat-Resina Research Associate Journal of Chemical Education and University of Wisconsin 209 N. Brooks St. Madison, WI 53715-1116 Tel: 608 8901702 // Fax: 608 2627145 e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat http://x.prat.resina.googlepages.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 Jmol-users@lists.sourceforge.net 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-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Xavier Prat-Resina Research Associate Journal of Chemical Education and University of Wisconsin 209 N. Brooks St. Madison, WI 53715-1116 Tel: 608 8901702 // Fax: 608 2627145 e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat http://x.prat.resina.googlepages.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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Hydrogen Bonds up on Motivated Proteins
Just a line to say that I've now traced the tortuous path from SQL, java servlet, Perl CGI, javascript, to Jmol scripting language and have my web application, Motivated Proteins ( http://motif.gla.ac.uk/ motif/index.html), showing the HBPlus Hydrogen Bonds from our dbase in the 3D - Single Motif Display of search results. Thanks for the help with the last link in the chain. David PS Comments and feedback welcome. ___ Dr. David P. Leader, Faculty of Biomedical Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 (0)141 330 5905 http://doolittle.ibls.gla.ac.uk/leader The University of Glasgow, charity number SC004401 ___ - 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] jmol doesn't work with openjdk in Debian
On Tue, Nov 18, 2008 at 10:54 PM, Angel Herráez [EMAIL PROTECTED] wrote: Hi Ondrej The applets at http://jmol.sourceforge.net/scripting/ are simpler than those in the 'atoms' demo page (they are inserted directly, without using Jmol.js and they also have the mayscript tag). So you can use that page for tests and for reporting back to the openjdk people. However, they may not be cross-browser-optimized as Jmol.js applets are (basically, the use of applet, object or embed tags for inserting the applet; I'm not sure if that would make a difference in your case). Wow, all those applets work perfectly in my browser. So the problem seems related to some communication between the applet and javascript, right? I haven't yet tried a different browser. So I'll report using the jmol demo pages as an example that doesn't work. But if they say that it is a problem in your applets, I'll get stuck again. :) Ondrej - 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
