## jmol-developers — Detailed discussions about the source code by and for Jmol developers

You can subscribe to this list here.

2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 Jan Feb Mar Apr May (20) Jun (13) Jul (45) Aug Sep (3) Oct (5) Nov (1) Dec (1) Jan (20) Feb (8) Mar (10) Apr (38) May (8) Jun (1) Jul Aug (8) Sep (45) Oct (116) Nov (195) Dec (67) Jan (94) Feb (84) Mar (23) Apr (21) May (246) Jun (100) Jul (23) Aug (54) Sep (73) Oct (166) Nov (52) Dec (46) Jan (138) Feb (175) Mar (194) Apr (76) May (423) Jun (412) Jul (127) Aug (133) Sep (172) Oct (273) Nov (192) Dec (272) Jan (178) Feb (178) Mar (97) Apr (76) May (138) Jun (57) Jul (130) Aug (88) Sep (168) Oct (61) Nov (52) Dec (120) Jan (37) Feb (259) Mar (426) Apr (175) May (299) Jun (135) Jul (79) Aug (145) Sep (390) Oct (142) Nov (98) Dec (50) Jan (52) Feb (129) Mar (77) Apr (84) May (122) Jun (91) Jul (39) Aug (62) Sep (63) Oct (95) Nov (67) Dec (69) Jan (72) Feb (41) Mar (107) Apr (22) May (28) Jun (33) Jul (68) Aug (144) Sep (39) Oct (123) Nov (78) Dec (24) Jan (58) Feb (45) Mar (78) Apr (95) May (50) Jun (82) Jul (52) Aug (46) Sep (102) Oct (42) Nov (94) Dec (59) Jan (48) Feb (102) Mar (190) Apr (69) May (68) Jun (106) Jul (126) Aug (46) Sep (87) Oct (66) Nov (136) Dec (92) Jan (83) Feb (25) Mar (46) Apr (18) May (24) Jun (30) Jul (17) Aug (21) Sep (45) Oct (107) Nov (61) Dec (35) Jan (33) Feb (34) Mar (46) Apr (38) May (84) Jun (58) Jul (40) Aug (82) Sep (21) Oct (74) Nov (20) Dec (10) Jan (55) Feb (57) Mar (45) Apr (77) May (18) Jun (9) Jul (6) Aug (10) Sep (33) Oct (29) Nov (48) Dec (25) Jan (17) Feb (15) Mar (35) Apr (22) May (17) Jun (25) Jul (32) Aug (16) Sep (43) Oct (16) Nov Dec (8) Jan (20) Feb (10) Mar (24) Apr (24) May (1) Jun (19) Jul (24) Aug Sep Oct Nov (3) Dec (14) Jan (5) Feb (7) Mar (1) Apr (5) May (39) Jun (14) Jul Aug (9) Sep (22) Oct (10) Nov (6) Dec (2) Jan Feb Mar Apr (11) May Jun (3) Jul (6) Aug (2) Sep Oct (2) Nov (6) Dec Jan (1) Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
S M T W T F S

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20
(7)
21
(2)
22

23

24

25

26

27

28

29

30

31
(1)

Showing 10 results of 10

 [Jmol-developers] code revision of user interface for the JSmol pop-up menu From: Angel Herráez - 2013-08-31 23:54:46 Attachments: text/plain coremenu_AH.zip Dear Bob, I've worked on some retouching of the user interface of the JSmol pop-up menu. I couldn't find what is the source file that produces this menu, so I downloaded the production file, http://chemapps.stolaf.edu/jmol/jsmol/j2s/core/coremenu.z.js dated 19-Aug-2013_17:25 and worked from that I am attaching - the original file (unpacked in some online beautifier´) - my modified file (unpacked) - a Unix diff file between them, for guidance I have tested in localhost and everything seems to behave well. My motivations: - make the CSS rules isolated, i.e. applied only to jmolPopupMenu and not to other jQuery.menu instances that might be in the page - make it more compact (less tall, much less wide) - avoid the separators being visually active elements (on hover) - apply greyed-out style to disabled elements (rather than translucency), and make them visually inactive to mouse hover - avoid the # change in the url (by removing the href; this also seems to make the checkboxes more responsive) (Note) - added a ">" sign to expandable menu items - removed some css code that is not used by jmolPopupMenu - a more standard layout of html label tags, ie not surrounding the input tag The CSS is rather simplified, which should make easier for page developers to override some rules if they need (e.g. for finger-based devices). Still, there's quite a deal of mystery in some rules inherited from jQueryUI. I cleared up all that looked safe. Hope you can incorporate the changes. I think it feels quite better. --Note--: I tried to replace the a tags by span with a specific class (after all, they are not hyperlinks nor anchors), but it does not work. Seems that other code in the js file (coming from JQuery UI menu I believe) relies on them being 'a' tags, and I'd rather not mess up with that code. A flat seems to be fine, even if not semantically pure. 
 Re: [Jmol-developers] JSmol and java.lang.Error From: Gareth Oakes - 2013-08-21 22:52:51 > From: Robert Hanson > Subject: Re: [Jmol-developers] JSmol and java.lang.Error > > It's a pretty simple solution. Really what the problem is is that both >Jmol > and MathJax are competing for the AJAX processing. For compatibility with > MathJax, make sure: [snip] Thanks Bob we'll try your suggestion! -Gareth 
 Re: [Jmol-developers] JSmol and java.lang.Error From: Gareth Oakes - 2013-08-21 22:19:13 > Date: Tue, 20 Aug 2013 09:28:37 -0500 > From: Robert Hanson > > Yes, that's an important issue. I'm not satisfied, either, for just this > reason. It's not an easy one, because it relates to the Java2Script > compiler we use. There are many extensions we do need to use - especially > in the number area. Not sure about JavaScript error processing, although > obviously we need to catch those for our own purposes. I think the problem is to do with the fact that for some reason the java.lang.Error object is over-writing the core Javascript Error object. I would expect the Java2Script should place java.lang.Error into its own object (eg. a javascript object called "Java"). I don't know anything about Java2Script though so there may be good reasons why that isn't the case. > If you point me to a problem page and point me to the bit of your MathJax > code that is problematic, I can see what I can do. Thanks for the offer Bob. I will send some samples to you off-list. Cheers, Gareth 
 Re: [Jmol-developers] JSmol and java.lang.Error From: Robert Hanson - 2013-08-20 16:27:23 Attachments: Message as HTML It's a pretty simple solution. Really what the problem is is that both Jmol and MathJax are competing for the AJAX processing. For compatibility with MathJax, make sure: 1) you are using dynamic loading of the applet -- no
 Re: [Jmol-developers] Jmol integration into Java application (scripting question) From: Robert Hanson - 2013-08-20 14:36:33 Attachments: Message as HTML Oh, yes, sure. If you want to use the file dialog, just change the setting of defaultDropScript to your liking. Something like: set defaultDropScript 'load "%FILE"; wireframe -0.2; vibration on see http://chemapps.stolaf.edu/jmol/docs/?ver=13.2#set_defaultdropscriptfor a more complex example. If you are using the JmolViewer interface, just add whatever you want to the load script and use JmolViewer.script() Bob On Tue, Aug 20, 2013 at 5:35 AM, Andrei Ionut Apopei < andrei_ionut1987@...> wrote: > > Dear Jmol developers, > > Currently I'm trying to integrate a Jmol functionality into a Java > application. So far I founded a good starting point at this link: > http://old.nabble.com/Integrating-Jmol-into-an-application-td31583044.html > . > > My OS: Windows 7 > Jmol version: 13.2.3 > > It works great, but I wanna know if it is possible to put some scripts > (specific zoom, atom selection, vibration on, and so on) to load at the > beginning (when the file load e.g. Caffeine.xyz). How can I achieve this? > > Thanks, > Andrei > > > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmol-developers@... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Larson-Anderson 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 
 Re: [Jmol-developers] JSmol and java.lang.Error From: Robert Hanson - 2013-08-20 14:31:54 Attachments: Message as HTML [you must be working with Gareth, right?] So what is MathJax, and what does it have to do with Jmol? Sounds interesting.... There are some general browser page-reloading issues with JavaScript in general. I think it can depend upon whether you press ENTER in the URL line or press whatever button does a reload. Looks to me like it handles memory differently. Not sure. Bob On Tue, Aug 20, 2013 at 4:52 AM, Geoffrey Rowland wrote: > Have not investigated this in any detail, but have also noticed a clash > between JSmol and MathJax in some circumstances - with MathJax displaying a > [Math Processing Error]. > > In case it helps with the diagnosis, here are the symptoms I have > observed. Behaviour is somewhat variable. Firefox appears least > susceptible, Chrome and IE more so. Sometimes a page reload fixes the > issue, sometimes it breaks a working display. The problem appears worse for > pages with more, or more complex, JSmol instances. So, perhaps related to > the relative load/processing times for JSmol and MathJax? Get the problem > whether MathJax is loaded locally or from CDN. > > Cheers > > Geoff > > > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmol-developers@... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Larson-Anderson 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 
 Re: [Jmol-developers] JSmol and java.lang.Error From: Robert Hanson - 2013-08-20 14:28:45 Attachments: Message as HTML Gareth, Right list for sure. Yes, that's an important issue. I'm not satisfied, either, for just this reason. It's not an easy one, because it relates to the Java2Script compiler we use. There are many extensions we do need to use - especially in the number area. Not sure about JavaScript error processing, although obviously we need to catch those for our own purposes. If you point me to a problem page and point me to the bit of your MathJax code that is problematic, I can see what I can do. Bob On Tue, Aug 20, 2013 at 12:12 AM, Gareth Oakes wrote: > Hi there, > > I'm not sure if this is the correction mailing list or not, but wanted to > report an issue with JSmol. We are working on integrating JSmol into a web > site which already uses MathJax and we ran into an incompatibility issue. > We have a crude workaround but I wanted to explore the root cause. > > I have discovered that upon execution of the JSmol getApplet() method, the > java2script Clazz system seems to replace the standard Javascript Error > object with a copy of java.lang.Error. This causes MathJax to fail because > it expects to have the standard Javascript Error object available. > > Why are objects in the global Javascript namespace being modified and is > there a way to prevent it? > > BTW I discovered this in test file "jsmol.htm" which ships with jsmol-13.3.3.zip. > My test environment was Chrome 28.0.1500.95 on Windows XP. > > Cheers, > Gareth Oakes > > > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmol-developers@... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Larson-Anderson 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 
 [Jmol-developers] Jmol integration into Java application (scripting question) From: Andrei Ionut Apopei - 2013-08-20 10:35:15 Attachments: Message as HTML   Dear Jmol developers, Currently I'm trying to integrate a Jmol functionality into a Java application. So far I founded a good starting point at this link: http://old.nabble.com/Integrating-Jmol-into-an-application-td31583044.html. My OS: Windows 7 Jmol version: 13.2.3 It works great, but I wanna know if it is possible to put some scripts (specific zoom, atom selection, vibration on, and so on) to load at the beginning (when the file load e.g. Caffeine.xyz). How can I achieve this? Thanks, Andrei 
 [Jmol-developers] JSmol and java.lang.Error From: Geoffrey Rowland - 2013-08-20 09:52:20 Attachments: Message as HTML Have not investigated this in any detail, but have also noticed a clash between JSmol and MathJax in some circumstances - with MathJax displaying a [Math Processing Error]. In case it helps with the diagnosis, here are the symptoms I have observed. Behaviour is somewhat variable. Firefox appears least susceptible, Chrome and IE more so. Sometimes a page reload fixes the issue, sometimes it breaks a working display. The problem appears worse for pages with more, or more complex, JSmol instances. So, perhaps related to the relative load/processing times for JSmol and MathJax? Get the problem whether MathJax is loaded locally or from CDN. Cheers Geoff 
 [Jmol-developers] JSmol and java.lang.Error From: Gareth Oakes - 2013-08-20 05:12:21 Attachments: Message as HTML Hi there, I'm not sure if this is the correction mailing list or not, but wanted to report an issue with JSmol. We are working on integrating JSmol into a web site which already uses MathJax and we ran into an incompatibility issue. We have a crude workaround but I wanted to explore the root cause. I have discovered that upon execution of the JSmol getApplet() method, the java2script Clazz system seems to replace the standard Javascript Error object with a copy of java.lang.Error. This causes MathJax to fail because it expects to have the standard Javascript Error object available. Why are objects in the global Javascript namespace being modified and is there a way to prevent it? BTW I discovered this in test file "jsmol.htm" which ships with jsmol-13.3.3.zip. My test environment was Chrome 28.0.1500.95 on Windows XP. Cheers, Gareth Oakes 

Showing 10 results of 10