Re: [Jmol-users] javascript command fails in Safari?
Hmmm, this morning, after rebooting my Mac, neither can I reproduce it. It is working fine now. Failure was 100% consistent yesterday. I'll see if I can discern what if anything put Safari into this mode. I have the Develop menu turned on, so access to Show Error Console. I was using that a lot yesterday but after using it today, Jmol's _javascript_ command still worked. (I find that Firefox's Error Console usually gives a more specific diagnosis of where a _javascript_ error is in the .htm/.js files.) Ah, here's a good possibility. I entered pause into the Jmol console a couple of times yesterday, then apparently had to use Force Quit of Safari to regain control. I didn't reboot after that, but it crossed my mind that it would have been a good idea. -Eric At 9/6/08, Dean Johnston wrote: I can't reproduce this - the _javascript_ command works just fine from the Jmol console for me on both Firefox and Safari for OS X. Dean On Fri, Sep 5, 2008 at 6:18 PM, Eric Martz [EMAIL PROTECTED] wrote: It appears to me that the _javascript_ command of Jmol does not work in Safari on Mac OS X. Examples, typed into the Jmol console: _javascript_ alert(hi) or _javascript_ alert(document.location.href) These display the alert in Firefox on Windows or Mac OS X, but not in Safari on Mac OS X. If this is a known limitation, I suggest that it be documented for the _javascript_ command in the Jmol reference manual. Thanks, Eric - 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 - 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] Getting a complete history/historyLevel
It is often useful to be able to see the complete command history in Jmol applet's console, including all commands in scripts and scripts called from scripts (second level). After trying a few ideas yesterday, I decided that set historyLevel 1 was the best I hit upon. (Are there other methods?) It appeared that this must be issued before the first script file is called. If it is issued within a script file, the subsequent commands seemed not to be reported. Not surprisingly, I notice that set historyLevel 1 gives the commands in script files only one level down, plus the commands at the top level (level 0 I guess). If a script file contains a script command invoking a second level script file, the commands in that second level script are not reported. So I tried set historyLevel 2. Now I get the commands in the second level script ONLY. The entire remainder of the history before and after (levels 0 and 1) is missing. Is there a set historyLevel setting that will report the entire command history at all levels? What are the possible values for set historyLevel N and what do they mean? Bob, it would be great to clarify the documentation on set historyLevel about the range of legal values, what they mean, how to get the entire history for all levels all at once, and that the set historyLevel command must be issued before the first script command is encountered -- or whatever is correct if I have it wrong. Thanks very much, -Eric - 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] Getting a complete history/historyLevel
set historylevel 2 works fine for me. It should work as you expected. But history was recording full scripts, not individual commands, so commands were out of order. This might have thrown you off. That's corrected now. On Sat, Sep 6, 2008 at 9:12 AM, Eric Martz [EMAIL PROTECTED]wrote: It is often useful to be able to see the complete command history in Jmol applet's console, including all commands in scripts and scripts called from scripts (second level). After trying a few ideas yesterday, I decided that set historyLevel 1 was the best I hit upon. (Are there other methods?) It appeared that this must be issued before the first script file is called. If it is issued within a script file, the subsequent commands seemed not to be reported. Not surprisingly, I notice that set historyLevel 1 gives the commands in script files only one level down, plus the commands at the top level (level 0 I guess). If a script file contains a script command invoking a second level script file, the commands in that second level script are not reported. So I tried set historyLevel 2. Now I get the commands in the second level script ONLY. The entire remainder of the history before and after (levels 0 and 1) is missing. Is there a set historyLevel setting that will report the entire command history at all levels? What are the possible values for set historyLevel N and what do they mean? Bob, it would be great to clarify the documentation on set historyLevel about the range of legal values, what they mean, how to get the entire history for all levels all at once, and that the set historyLevel command must be issued before the first script command is encountered -- or whatever is correct if I have it wrong. Thanks very much, -Eric - 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] javascript command fails in Safari?
better to fix that. On Fri, Sep 5, 2008 at 8:18 PM, Eric Martz [EMAIL PROTECTED]wrote: It appears to me that the javascript command of Jmol does not work in Safari on Mac OS X. Examples, typed into the Jmol console: javascript alert(hi) or javascript alert(document.location.href) These display the alert in Firefox on Windows or Mac OS X, but not in Safari on Mac OS X. If this is a known limitation, I suggest that it be documented for the javascript command in the Jmol reference manual. Thanks, Eric - 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] javascript command fails in Safari?
sorry - missed some of those messages. OK, I'll assume the javascript command is working ok. As for pause -- that would be a threading issue. But pause is working fine for me on Mac OS-X. Bob On Sat, Sep 6, 2008 at 10:00 AM, Robert Hanson [EMAIL PROTECTED] wrote: better to fix that. On Fri, Sep 5, 2008 at 8:18 PM, Eric Martz [EMAIL PROTECTED]wrote: It appears to me that the javascript command of Jmol does not work in Safari on Mac OS X. Examples, typed into the Jmol console: javascript alert(hi) or javascript alert(document.location.href) These display the alert in Firefox on Windows or Mac OS X, but not in Safari on Mac OS X. If this is a known limitation, I suggest that it be documented for the javascript command in the Jmol reference manual. Thanks, Eric - 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 -- 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] javascript command fails in Safari?
In my previous message on this thread, I agreed that Jmol's javascript command was working in Safari on OS X. However, as I continue to test this code today, sometimes it stops working for no apparent reason. Once it stops, it seems to fail repeatably until I quit and restart Safari. When it stops working, if the Jmol console is open and debugscript is on, the javascript command appears in the console, but the results of that javascript do not occur. I have not managed to examine the Java console when this is happening. So I am getting intermittant failures. So I have decided not to rely on Jmol's javascript command. Instead I use Jmol's message command to send a unique message, trap that in messageCallback, and use that to trigger the desired javascript code. I have used messageCallback extensively and have never found any issues with it. If anyone else observes this intermittant failure of Jmol's javascript command in Safari, I suggest that this be mentioned as a caution in the Jmol documentation entry on javascript. My OS X and Safari are up to date: 10.5.4 and 3.1.2 respectively. I am using Jmol applet 11.6.RC12. -Eric At 9/6/08, Dean Johnston wrote: I can't reproduce this - the javascript command works just fine from the Jmol console for me on both Firefox and Safari for OS X. Dean On Fri, Sep 5, 2008 at 6:18 PM, Eric Martz mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] wrote: It appears to me that the javascript command of Jmol does not work in Safari on Mac OS X. Examples, typed into the Jmol console: javascript alert(hi) or javascript alert(document.location.href) These display the alert in Firefox on Windows or Mac OS X, but not in Safari on Mac OS X. If this is a known limitation, I suggest that it be documented for the javascript command in the Jmol reference manual. Thanks, Eric - 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=/http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list mailto:Jmol-users@lists.sourceforge.netJmol-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 - 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 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ - 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] javascript command fails in Safari?
yes, that's a far better solution anyway. The javascript command cannot be used with the signed applet in any command that also accesses files -- script, load, echo IMAGE. I had to do something like that in Jmol Protein Explorer as well. You have to be very careful with more complex scripts that you aren't mixing these two modes -- javascript commands and file reading -- in the same script thread. That's one of the reasons I implement the change that # comments are not simply ignored but instead processed as commands and sent to the script callback function. That's definitely the way to go with complex scripts like yours, Eric. Eric, are you using the signed or unsigned applet? Bob On Sat, Sep 6, 2008 at 10:45 AM, Eric Martz [EMAIL PROTECTED]wrote: In my previous message on this thread, I agreed that Jmol's javascript command was working in Safari on OS X. However, as I continue to test this code today, sometimes it stops working for no apparent reason. Once it stops, it seems to fail repeatably until I quit and restart Safari. When it stops working, if the Jmol console is open and debugscript is on, the javascript command appears in the console, but the results of that javascript do not occur. I have not managed to examine the Java console when this is happening. So I am getting intermittant failures. So I have decided not to rely on Jmol's javascript command. Instead I use Jmol's message command to send a unique message, trap that in messageCallback, and use that to trigger the desired javascript code. I have used messageCallback extensively and have never found any issues with it. If anyone else observes this intermittant failure of Jmol's javascript command in Safari, I suggest that this be mentioned as a caution in the Jmol documentation entry on javascript. My OS X and Safari are up to date: 10.5.4 and 3.1.2 respectively. I am using Jmol applet 11.6.RC12. -Eric At 9/6/08, Dean Johnston wrote: I can't reproduce this - the javascript command works just fine from the Jmol console for me on both Firefox and Safari for OS X. Dean On Fri, Sep 5, 2008 at 6:18 PM, Eric Martz mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] wrote: It appears to me that the javascript command of Jmol does not work in Safari on Mac OS X. Examples, typed into the Jmol console: javascript alert(hi) or javascript alert(document.location.href) These display the alert in Firefox on Windows or Mac OS X, but not in Safari on Mac OS X. If this is a known limitation, I suggest that it be documented for the javascript command in the Jmol reference manual. Thanks, Eric - 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=/ http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Jmol-users mailing list mailto:Jmol-users@lists.sourceforge.netJmol-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 - 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 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Re: [Jmol-users] Problems with echo images image buttons
Eric, That script is way too complex for me to reproduce here, but I did fix the echo alignment. There were a couple of bugs there, particularly with the y-offset of centered echos. All should be fixed. I'll see if we can get RC13 out this weekend so you can check it. Anything else you are finding? Bob On Fri, Sep 5, 2008 at 4:25 PM, Eric Martz [EMAIL PROTECTED]wrote: Hi, Bob, This does not have to work in 11.6 (final release). On April 13, 2007, you announced that echos can be made into buttons that, when clicked, execute a specified script, giving this example: http://chemapps.stolaf.edu/jmol/docs/examples-11/buttons.htm This works fine for me. I can use this for now. The manual states that an image file can be displayed as an echo. I am trying to combine the two: display an image of a button, and have it respond to a click by executing a specified script. Because it will look like a button, I can avoid the long label that I might think best with a text echo Click Here to Center All, just labeling the button Center All. Plus, it will be more intuitive -- and COOL! I am having several problems displaying the image correctly, and these also keep the portion of the image that is clickable to be very tiny. I have placed a demo listing the issues here: http://www.bioinformatics.org/jmol-tutorials/jtat_2008_08_05/jtatdemo/test1/contents.htm Thanks, -Eric - 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] javascript command fails in Safari?
Not sure that it has anything to do with Eric's problem, but remember when using Jmol and Safari to look at the Mac's own Console application (lives in utilities, but I keep it in my dock) for Jmol output. David ___ 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
[Jmol-users] echo/set echo/color echo documentation
Whenever I use echos, I get confused, and spend extra time discerning how they work. I would like to suggest that the documentation be improved by adding explicit statements of echo behavior to make the following points. It appears to me that some but not all set echo commands accept the name of an echo. set echo top left, set echo all/display/hidden/none/off apparently do not accept an echo name, if the documentation is correct. It might be useful, in the documentation, to separate the set echo commands into two sections, explicitly stating that one section accepts an echo name and the other does not. It appears to me that while echo commands do not accept a name, they obey prior set echo commands, placing the echoed text into only the currently set echo name. It appears to me that color echo and color echo background commands spill forward (from the currently named echo to subsequently set echo names) but do not spill backwards to previously set echo names. This is OK but can be unexpected and confusing. Thus, in order to have different colors in an echo that follows an explicitly colored echo, one must explicitly color the new echo, or set its colors to none. If the first thing after echo is #, no text is echoed. If the # follows some text, e.g. echo hello # goodbye the comment is echoed. However if the echo text is quoted, then the following comment is not echoed. Again, OK, but could be confusing. I think this script demonstrates all these principles, and could be put into the documentation as an example. set echo off background white set echo myecho1 0% 100% echo 1 Default Colors set echo myecho2 40% 100% #color echo myecho2 yellow NAME NOT ACCEPTED color echo yellow color echo background green echo 2 Explicit Colors set echo myecho3 100% 100% echo 3 Inherits Colors set echo myecho4 0% 90% color echo red color echo background pink echo 4 Explicit Colors set echo myecho5 40% 90% color echo blue echo 5 Explicit Text, Inherits Bkg set echo myecho6 100% 90% color echo none color echo background none echo 6 Explicit Colors None set echo myecho7 0% 80% color echo black echo #comment7 set echo myecho8 40% 80% echo comment 8A #comment 8B set echo myecho9 100% 80% echo comment 9A #comment98B - -Eric - 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] echo vs. hover?
In the documentation, the sections on echo and set echo say See also: hover. At the section on hover, I don't see anything about echo, except See also: echo. Can echos have hovers? How? -Eric - 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] Dynamic base64 decoding
Hi Bob,
Aha, jmolScriptwait ? that?s the ticket!
Yeah, I know about the MSIE issue, and I?m trying to deal with that
now. Here?s the issue: I'm adding the jmol applet images dynamically
to the open webpage, as opposed to exporting to another window as does
Angel?s code (and very nicely too).
My code for MSEI looks like this:
if (nav64=='nocomp'){
var testimg=document.getElementById(SnpShtImg)
var imgB64 = image/jpeg;base64, + jmolGetPropertyAsString('image');
var B64path=base64.php
testimg.src = B64path + ? + imgB64;
}
Which calls Dean Edwards original base64.php code.
It doesn?t work; the img appears empty.
Yet if I manually feed a base64-encoded image (such as this from Dean
Edwards web page), it does work.
imgB64=data:image/gif;base64,R0lGODlhDwAPAKECzMzM/wAAACwADwAPAAACIISPeQHsrZ5ModrLlN48CXF8m2iQ3YmmKqVlRtW4MLwWACH+H09wdGltaXplZCBieSBVbGVhZCBTbWFydFNhdmVyIQAAOw==;
Could the issue be the size of the jmol-derived image?
Thinking about this from another angle? is there a technical reason
why jmol cannot deliver a non-base64 encoded image that could be
dynamically added to the open web page: something like
testimg.src=jmolGetImage (?jpeg?)?
(Have I just fully revealed my lack of understanding of JAVA, or,
is this already possible and I have once again missed it in the
documentation?)
Steve
--
Steven R. Spilatro
Dept of Biology and Environmental Science
Marietta College
Marietta, OH
This message was sent using Marietta College WebMail.
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Re: [Jmol-users] javascript command fails in Safari?
No problems on Safari here. On 6 Sep 2008, at 16:58, [EMAIL PROTECTED] wrote: If anyone else observes this intermittant failure of Jmol's javascript command in Safari, I suggest that this be mentioned as a caution in the Jmol documentation entry on javascript. My OS X and Safari are up to date: 10.5.4 and 3.1.2 respectively. I am using Jmol applet 11.6.RC12. All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) - 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] javascript command fails in Safari?
Hi Eric, I do observe the same behaviour on at least one project I work on. But it behaves the same in Firefox 3.0 as well. Paul If anyone else observes this intermittant failure of Jmol's javascript command in Safari, I suggest that this be mentioned as a caution in the Jmol documentation entry on javascript. My OS X and Safari are up to date: 10.5.4 and 3.1.2 respectively. I am using Jmol applet 11.6.RC12. -Eric - 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] cgi and Jmol
Hello: I just tried to run a Jmol java script inside a html document from a cgi output, but I got an error (Exec format error). I pasted the same html code generated from cgi output and it works perfectly, so it seems I should take another thing into account trying to invoke a java script from the cgi output and dont have any idea what it is. It will be very helpful to me if any of you can help me. Thank you A. - 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] cgi and Jmol
Dear Avenha, there is absolutely nothing special about cgi output. Hard to say what you mean by a Jmol java script inside an HTML document. pasted the code to what? Can you send an example or point us to a page? The main thing is to have Jmol.js in the right place and have Jar and model files appropriately placed as well. Also, a common error is capitalization. On your hard drive capitalization of file names doesn't matter; on the server it will. First thing is to find the Java console on your client and see what it is telling you. Clip that message and send it by email to this list. Bob Hanson On Sat, Sep 6, 2008 at 5:21 PM, avehna [EMAIL PROTECTED] wrote: Hello: I just tried to run a Jmol java script inside a html document from a cgi output, but I got an error (Exec format error). I pasted the same html code generated from cgi output and it works perfectly, so it seems I should take another thing into account trying to invoke a java script from the cgi output and dont have any idea what it is. It will be very helpful to me if any of you can help me. Thank you A. - 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] Dynamic base64 decoding
I don't think you can put that many bytes on a URL line. Better would be to
put the base64 data into a textarea in a form and submit it using
method=post. Even that might have some limitations.
Bob
On Sat, Sep 6, 2008 at 12:19 PM, [EMAIL PROTECTED] wrote:
Hi Bob,
Aha, jmolScriptwait ? that?s the ticket!
Yeah, I know about the MSIE issue, and I?m trying to deal with that now.
Here?s
the issue: I'm adding the jmol applet images dynamically to the open
webpage, as opposed to exporting to another window as does Angel?s code (and
very nicely too).
My code for MSEI looks like this:
if (nav64=='nocomp'){
var testimg=document.getElementById(SnpShtImg)
var imgB64 = image/jpeg;base64, + jmolGetPropertyAsString('image');
var B64path=base64.php
testimg.src = B64path + ? + imgB64;
}
Which calls Dean Edwards original base64.php code.
It doesn?t work; the img appears empty.
Yet if I manually feed a base64-encoded image (such as this from Dean
Edwards web page), it does work.
imgB64=data:image/gif;base64,R0lGODlhDwAPAKECzMzM/wAAACwADwAPAAACIISPeQHsrZ5ModrLlN48CXF8m2iQ3YmmKqVlRtW4MLwWACH+H09wdGltaXplZCBieSBVbGVhZCBTbWFydFNhdmVyIQAAOw==;
Could the issue be the size of the jmol-derived image?
Thinking about this from another angle? is there a technical reason why
jmol cannot deliver a non-base64 encoded image that could be dynamically
added to the open web page: something like testimg.src=jmolGetImage
(?jpeg?)?
(Have I just fully revealed my lack of understanding of JAVA, or, is this
already possible and I have once again missed it in the documentation?)
Steve
--
Steven R. Spilatro
Dept of Biology and Environmental Science
Marietta College
Marietta, OH
This message was sent using Marietta College WebMail.
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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
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Re: [Jmol-users] echo vs. hover?
Eric, No, it just means they are related. That's all. Nico has released 11.6.RC13, so please check out my bug fixes. Thanks, Nico! Bob On Sat, Sep 6, 2008 at 11:42 AM, Eric Martz [EMAIL PROTECTED]wrote: In the documentation, the sections on echo and set echo say See also: hover. At the section on hover, I don't see anything about echo, except See also: echo. Can echos have hovers? How? -Eric - 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
