Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Nicolas Vervelle
On Fri, Oct 10, 2008 at 1:00 AM, Robert Hanson <[EMAIL PROTECTED]> wrote: > However, if a file is missing, then the server is going to send a "no file > found" message that is going to cause a Jmol crash. > Not good. Since we have the list of languages in GT, we could try to get the file only if

Re: [Jmol-developers] MD trajectories for 11.7

2008-10-09 Thread Robert Hanson
Hey, Matt, you might be in luck. On Thu, Oct 9, 2008 at 2:01 PM, Matthew Zwier <[EMAIL PROTECTED]> wrote: > > > > At least, I think you can Supposed to be able to. You are just > limited > > to one trajectory step from EACH sequence loaded. I can't imagine why > that > > would take any major

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Robert Hanson
all OK for me. Except I'm having that same problem I've had before with Eclipse not properly indicating which options I've selected for the ant build. I was able nonetheless to get both applets made as well as the application, and everything works as advertised. Each language jar file is read off t

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Angel Herráez
I've done a local build from revision 10030 and the unsigned applet seems to work OK; opens in Spanish, changes languages from the popup menu withou a hitch (I'd even say that quicker than before). I tried English, French, Portuguese, back to Spanish. However, the app gets hung at the "Initia

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Nicolas Vervelle
Modifications done, it really needs some testing (I haven't tested the applet) Nico On Thu, Oct 9, 2008 at 3:47 PM, Nicolas Vervelle <[EMAIL PROTECTED]>wrote: > Ok, I will commit some modifications this evening. > > With the modifications I have made (GT.java and build-i18n.xml), Jmol.jar > is w

Re: [Jmol-developers] MD trajectories for 11.7

2008-10-09 Thread Matthew Zwier
Hi Bob, On Thu, Oct 9, 2008 at 10:10 AM, Robert Hanson <[EMAIL PROTECTED]> wrote: > Matt, good to hear this! Comments below. - Bob > >> 1) Are there plans to support simultaneous display of multiple >> trajectories? > > The big issue is memory. Jmol can handle about 120,000 atoms (at least on my

Re: [Jmol-developers] /trunk/Jmol/src/org/jmol/i18n/GT.java - English variant names

2008-10-09 Thread Robert Hanson
Actually, the order is just the order in the list in code: languageList = new Language[] { new Language("ca",GT._("Catalan"), true), new Language("cs",GT._("Czech"),true), new Language("da",GT._("Danish"), fal

[Jmol-developers] /trunk/Jmol/src/org/jmol/i18n/GT.java - English variant names

2008-10-09 Thread Angel Herráez
In revision 10022, dleidert has changed the tags for languages (used in the pop-up menu) I also think this sounds better this way, but there is a side effect: as far as I can see, Jmol orders the entries in the language menu alphabetically. With the new tags, both English variants will likely

Re: [Jmol-developers] MD trajectories for 11.7

2008-10-09 Thread Robert Hanson
Matt, good to hear this! Comments below. - Bob On Wed, Oct 8, 2008 at 10:09 PM, Matthew Zwier <[EMAIL PROTECTED]> wrote: > Hi all, > > A few days ago, Bob Hanson mentioned that improved support for display > of MD trajectories is on the docket for 11.7. I'm interested in > surveying the lay of

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Nicolas Vervelle
Ok, I will commit some modifications this evening. With the modifications I have made (GT.java and build-i18n.xml), Jmol.jar is working correctly and probably JmolApplet.jar also. I have to modify the build process for the splitted applet jars. I have planned to use a loop for the jars (like in b

Re: [Jmol-developers] reading Amber MD files: wrong element identification PA, PB

2008-10-09 Thread Robert Hanson
was there a URL reference for that topology file? On Thu, Oct 9, 2008 at 8:43 AM, Robert Hanson <[EMAIL PROTECTED]> wrote: > easy enough. There is an algorithm that just needs to be augmented. If > there's a definitive way of doing this, I'm all ears. > > Bob > > > > On Thu, Oct 9, 2008 at 4:57 A

Re: [Jmol-developers] reading Amber MD files: wrong element identification PA, PB

2008-10-09 Thread Robert Hanson
easy enough. There is an algorithm that just needs to be augmented. If there's a definitive way of doing this, I'm all ears. Bob On Thu, Oct 9, 2008 at 4:57 AM, Angel Herráez <[EMAIL PROTECTED]> wrote: > I have being able to test successfully some MD files from Amber using > 11.7.1 It works ver

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Robert Hanson
OK, that sounds fine. We'll go with multiple JAR files. As I recall, we need to: 1) just include all subdirectory business in Jmol.jar and JmolApplet.jar (no changes there?) 2) JmolApplet0.jar and JmolAppletSigned0.jar -- We need to check to see if we need separate manifests for each translation

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Robert Hanson
Henry, I think there has to be a balance between allowing new features and preserving the integrity of the initial publication. The nightmare of some upgrade breaking a published work is disturbing. An author has published what they published. I'm not sure it would be appropriate to automatically a

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Nicolas Vervelle
Hi, On Wed, Oct 8, 2008 at 11:19 PM, Robert Hanson <[EMAIL PROTECTED]> wrote: > They have to be in separate packages. Once one class of a package is > accessed, all classes of that package must be loaded. So each has to be in > its own package. It's own name space. > Ok, it's easy to do by putti

Re: [Jmol-developers] Problems translating and importing in Launchpad

2008-10-09 Thread Nicolas Vervelle
Hi, The error message on launchpad is not very clear about what is wrong, but the fix is quite simple : use two single quotes (instead of one) when there's a parameter. I don't remember the exact reason, but quotes have special meaning in .po files. So, the translation for the first message shoul

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Angel Herráez
A few comments/ideas raised by Henry's post: > I also suspect that there must be a very wide spread of versions in that > embedding, possibly going back to Jmol 10 and even earlier. My experience is > that Jmol has excellent backward compatibility, and that there is a high > probability that

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Rolf Huehne
Rzepa, Henry wrote: > Egon has just posted download statistics for Jmol to the users list. > > I suspect Jmol has been embedded in 100s, if not 1000s (or even 10Ks worth) > of journal pages. I also suspect that there must be a very wide spread of > versions in that embedding, possibly going b

Re: [Jmol-developers] page needs updating

2008-10-09 Thread Angel Herráez
I have commited the update to display 11.6 as current version nr. in the front page and the update of the applet files for the website. I want to check that the examples/demos work well, but I cannot do that right now locally due to the applet path, so I'll test them once the changes are in the

[Jmol-developers] reading Amber MD files: wrong element identification PA, PB

2008-10-09 Thread Angel Herráez
I have being able to test successfully some MD files from Amber using 11.7.1 It works very well. I will post the example soon --it may well be run across the web, as the 4 files sum 1.5MB gzipped, or at least serve as test files for the collection. However, I am havign a little problem that seem

Re: [Jmol-developers] Jmol 11.6 for the record

2008-10-09 Thread Rzepa, Henry
Egon has just posted download statistics for Jmol to the users list. I suspect Jmol has been embedded in 100s, if not 1000s (or even 10Ks worth) of journal pages. I also suspect that there must be a very wide spread of versions in that embedding, possibly going back to Jmol 10 and even earlie