Re: [Jmol-users] Jmol demo page hangs
Hello Bob, I see the same thing with Firefox and XP. I notice that the page source ends coordinate file lines with \n - linefeed. I wonder if this is a cr/lf issue. I run into this problem frequently. I'm not sure about a cross platform solution, but I wonder is ending the lines with \r\n would work on your system. Alternatively, I've had luck with loading an inline file from the JME applet into Jmol with the following direct approach: document.getElementById(MyAppleName).loadInlineString(jmeString, hover %a atomno=%i;echo;isosurface '';mo translucent;isosurface translucent;, false); Ignoring my load script, jmeString is simply the un-doctored coordinate string (molfile) from JME - i.e. no concatenated LF or CR/LF. Otis -- Otis Rothenberger http://chemagic.org On Wed, Jan 13, 2010 at 1:12 PM, Grossman, Robert B robert.gross...@uky.edu wrote: Hi, I'm trying to figure out how to load molecular structures into Jmol from JavaScript variables (instead of files). When I go to the demo page http://jmol.sourceforge.net/demo/jssample2/ , Jmol fails to load. That is, it says, Loading Jmol applet ... and the clock begins, but it never finishes loading. ??? -- Bob -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ 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 Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol demo page hangs
Thanks for your help, Otis. Unfortunately, your approach won't work for me; we acquire the data from a Java variable whose value in turn we acquire from a database. We use MOL files in Javascript variables with \n at the end of each line as input for other applets, e.g., MarvinSketch and MarvinView. So I think this is not a platform problem, but a Jmol problem. From: Otis Rothenberger o...@chemagic.com Reply-To: jmol-users@lists.sourceforge.net Date: Wed, 13 Jan 2010 13:47:56 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] Jmol demo page hangs Subject: Re: [Jmol-users] Jmol demo page hangs Hello Bob, I see the same thing with Firefox and XP. I notice that the page source ends coordinate file lines with \n - linefeed. I wonder if this is a cr/lf issue. I run into this problem frequently. I'm not sure about a cross platform solution, but I wonder is ending the lines with \r\n would work on your system. Alternatively, I've had luck with loading an inline file from the JME applet into Jmol with the following direct approach: document.getElementById(MyAppleName).loadInlineString(jmeString, hover %a atomno=%i;echo;isosurface '';mo translucent;isosurface translucent;, false); Ignoring my load script, jmeString is simply the un-doctored coordinate string (molfile) from JME - i.e. no concatenated LF or CR/LF. Otis -- Otis Rothenberger http://chemagic.org On Wed, Jan 13, 2010 at 1:12 PM, Grossman, Robert B robert.gross...@uky.edu wrote: Hi, I'm trying to figure out how to load molecular structures into Jmol from JavaScript variables (instead of files). When I go to the demo page http://jmol.sourceforge.net/demo/jssample2/ , Jmol fails to load. That is, it says, Loading Jmol applet ... and the clock begins, but it never finishes loading. ??? -- Bob -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ 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 Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ 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 Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol demo page hangs
Bob G., thanks for reporting this. I've run a quick check with a local copy of the offending page, and it's not an issue of linefeeds. It's a bug in Jmol. I can trace it back to between 11.8.7 and 11.8.11. 11.8.15 (the current version at the website) and 11.9.13 fail too. jmolLoadInline() works fine even with 11.8.15. It's just jmolAppletInline() that has the problem. If you change it to jmolAppletInline(200, ) then the radio buttons that call jmolLoadInline() work fine. And I've done all that using the Jmol.js of 11.8.15, so it's not a Jmol.js bug -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol demo page hangs
I've narrowed it down to between 11.8.10 (works) and 11.8.11 (fails). That's 20 to 28 nov. 2009 -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol demo page hangs
Thanks Angel. I've changed my invocation of Jmol as follows:
script type=text/javascript
jmolInitialize('%= pathToRoot %nosession/jmol');
jmolApplet([250, 250]);
jmolLoadInline('%= Utils.toValidJS(calcResults) %');
/script
It compiles at runtime as,
jmolInitialize('../../nosession/jmol');
jmolApplet([250, 250]);
jmolLoadInline('\n Marvin 10270415522D\n\n 9 9 0 0 0 0
999 V2000\n -2.24570.81880. C 0 0 0 0 0 0 0 0
0 0 0 0\n -2.2457 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0
0\n -1.5313 -0.41880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.8168 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8168
0.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.10231.2313
0. O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.53131.2313
0. C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.53132.88130. C
0 0 0 0 0 0 0 0 0 0 0 0\n -1.53132.05630. C 0 0
0 0 0 0 0 0 0 0 0 0\n 7 1 1 0 0 0 0\n 7 5 2 0 0 0 0\n 1
2 2 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 2 0 0 0 0\n 4 5 1 0
0 0 0\n 5 6 1 0 0 0 0\n 8 9 1 0 0 0 0\n 7 9 1 0 0 0 0\nM
APO 1 9 1\nM STY 1 1 SUP\nM SAL 1 2 8 9\nM SBL 1 1 9\nM
SMT 1 Et\nM END\n');
/script
But although it now appears to load, I don't see a molecule in the viewer.
Furthermore, if I try to open another Jmol applet (with the first page open or
closed), Safari hangs.
From: Angel Herráez angel.herr...@uah.es
Reply-To: jmol-users@lists.sourceforge.net
Date: Wed, 13 Jan 2010 14:26:28 -0500
To: jmol-users@lists.sourceforge.net
Conversation: [Jmol-users] Jmol demo page hangs
Subject: Re: [Jmol-users] Jmol demo page hangs
Bob G., thanks for reporting this.
I've run a quick check with a local copy of the offending page, and it's not an
issue of
linefeeds.
It's a bug in Jmol. I can trace it back to between 11.8.7 and 11.8.11.
11.8.15 (the current version at the website) and 11.9.13 fail too.
jmolLoadInline() works fine even with 11.8.15.
It's just jmolAppletInline() that has the problem.
If you change it to
jmolAppletInline(200, )
then the radio buttons that call jmolLoadInline() work fine.
And I've done all that using the Jmol.js of 11.8.15, so it's not a Jmol.js bug
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Re: [Jmol-users] Jmol demo page hangs
Yes, I see the same: the applet ends loading, but stays empty. Try changing to JmolApplet 11.8.10 It works for me with your code -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol demo page hangs
Thanks, it displays now. From: Angel Herráez angel.herr...@uah.es Reply-To: jmol-users@lists.sourceforge.net Date: Wed, 13 Jan 2010 15:28:46 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] Jmol demo page hangs Subject: Re: [Jmol-users] Jmol demo page hangs Yes, I see the same: the applet ends loading, but stays empty. Try changing to JmolApplet 11.8.10 It works for me with your code -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ 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 Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol demo page hangs
It's a bug. I've fixed it. Please check http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip On Wed, Jan 13, 2010 at 12:12 PM, Grossman, Robert B robert.gross...@uky.edu wrote: Hi, I'm trying to figure out how to load molecular structures into Jmol from JavaScript variables (instead of files). When I go to the demo page http://jmol.sourceforge.net/demo/jssample2/ , Jmol fails to load. That is, it says, Loading Jmol applet ... and the clock begins, but it never finishes loading. ??? -- Bob -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ 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 Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
