Re: [Jmol-users] weird problem launching minimization

2010-06-10 Thread Philip Bays
And a wired one at that. Turns out that I have 10 associated tutorials. A friend on a PC could not get any of them to load. I have set one of them to use the signed applet. The others still call the unsigned. If she uses the one with the signed applet first, all of the others load with no pr

Re: [Jmol-users] weird problem launching minimization

2010-06-10 Thread Robert Hanson
Sounds like a Java bug. On Tue, Jun 8, 2010 at 7:43 PM, Philip Bays wrote: > Bob: I think I do not understand signed applets, or at least not this one. > > I set one of my HTML files to call the signed applet. It calls it and > gives me the signed applet dialog. As I look at it I have three >

Re: [Jmol-users] weird problem launching minimization

2010-06-09 Thread Angel Herráez
I stand corrected: Angel wrote: > It fixes the script file loading, but not the minimize from a button. The plain "minimize" DOES work after the fix, the problem is in using a messageCallback to follow the minimization process. Sorry to bother you all with so many messages, but this is frustra

Re: [Jmol-users] weird problem launching minimization

2010-06-09 Thread Angel Herráez
Bob wrote: > jmolSetCallback("UseCommandThread","true") Thanks, Bob, that's great! It fixes the script file loading, but not the minimize from a button. I'm compiling more detailed testing, but for now (applies to both Firefox and IE8 in WinXP): Description of folder locations, relative to the

Re: [Jmol-users] weird problem launching minimization

2010-06-09 Thread Angel Herráez
El 8 Jun 2010 a las 20:43, Philip Bays escribió: > I set one of my HTML files to call the signed applet. It calls it > and gives me the signed applet dialog. As I look at it I have three > choices -- run, cancel, or always trust. I understand Run and Always > trust. But I assumed that Cancel mea

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Philip Bays
Bob: I think I do not understand signed applets, or at least not this one. I set one of my HTML files to call the signed applet. It calls it and gives me the signed applet dialog. As I look at it I have three choices -- run, cancel, or always trust. I understand Run and Always trust. But I

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Robert Hanson
OK, THERE IS A WORK-AROUND: jmolInitialize jmolSetCallback("UseCommandThread","true") jmolApplet As far as I can tell, this brings you back to the old behavior. The JAR files can be anywhere, and the files Jmol reads can be anywhere in or beneath the JAR file directory. For example: jmol

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Angel Herráez
Phil, so my suspicion that your problem and mine has the same scent are taking form. Java security errors come from folder layouts. I've changed mine and hit a problem, you have changed yours and hit another problem. Everything seems to com from the same cause. We are needing folder system dr

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Philip Bays
Bob: I think this may be a stupid question, but.. I understand your nomenclature diagram. Are you saying that the pages directory must be inside the jmol directory which itself must be at the root (top level) of the site. That is, that you must past through the jmol directory to get to the

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Angel Herráez
> > Actually, the solution looks like using this path set: > > /jmol > > .[all jar files here] > > ./pages > > .[html here] Not even that, or I may be coming blind. Fails in both Firefox, IE8, Chrome. Works in Safari (all Win) Page is at etc\Jmol-12.0.RC

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Angel Herráez
> OK, looks like there is a new Firefox security policy: I will double-check again, but I think that IE is doing me the same. > For all local files accessed via JavaScript, both the JAR file AND > the HTML file must be on the path to that file. Jmol files in a folder BELOW the html page works t

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Robert Hanson
OK, looks like there is a new Firefox security policy: For all local files accessed via JavaScript, both the JAR file AND the HTML file must be on the path to that file. Pretty sure that's new. The fix for me was to move the Jmol-12 directory into the pages directory, modify the files, and i

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Angel Herráez
Thanks, Bob. I'm rather puzzled I think that all has started when I changed from having Jmol files below the page folder to having them on a sister folder. The script files are always with Jmol or below it. So it's the position relative to the html that makes the difference. Comparing to the a

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Robert Hanson
UFF.txt is a resource within the Jar file. Specifically it is in: JmolApplet0_Minimize.jar/org/jmol/minimize/forcefield JmolAppletSigned0_Minimize.jar/org/jmol/minimize/forcefield If you use set debug you should see its contents listed when the minimizer runs. Very odd that the system can't

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Angel Herráez
This is the summary and a test case: 1. Problem is there only for local files, not from server. Seems to be related to Jmol reading text files (either scripts or the UFF.txt file embedded somehow inside Jmol) from a folder where the applet jars are but the webpage is not. Main_folder |

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Angel Herráez
Further, even accounting for tricky security policies, I cannot imagine why the very same command works from the console, and what has minimize to do with the security. (minimize is also failing from a button, not from console or popup menu) --

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Angel Herráez
Phil, I don't know. I'm starting to see ghosts :-) I've just made a simple page and gone back to Jmol 11.6, just to confirm this is or not an issue of recent Jmol versions. It is not. The command that fails when called in a button is OK when entered at the console. The paths are correct, the Ja

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Philip Bays
Angel: Are your issue and mine related? I use a random number generator to choose which file to load. The first one is loaded fine. But when I push a button to reload (another random numbered file), I get the exception. Phil On Jun 8, 2010, at 6:57 AM, Angel Herráez wrote: > The same probl

Re: [Jmol-users] weird problem launching minimization

2010-06-08 Thread Angel Herráez
The same problem stays in 12.0.RC17 and I'm finding more strange behaviours that, altough unrelated in principle, may have the same origin: I am calling a script file (that acts on the current model, does not load anything). When invoked from a button in the page, if raises a Java security err

[Jmol-users] weird problem launching minimization

2010-06-07 Thread Angel Herráez
I still need to narrow down the problem, but I'm seeing something strange with 12.0.RC16 that wasn't there in (quite) previous versions. Does it ring a bell or should I go on narrowing the exact circumstances? Applet, message callback is active (to report about the ongoing minimization) I act