Re: [Jmol-users] Fwd: installing JSmol extension

Bob, The path is http://dipc.ehu.es/bondslam/images/b/b4/CH3F_mo10.cub.jvxl which is the path in the script, with lower case i for images http://dipc.ehu.es/bondslam/Images/b/b4/CH3F_mo10.cub.jvxl has an upper case I for Images and the file system is case sensitive. Henry Rzepa, http://orc

[Jmol-users] Fwd: installing JSmol extension

The page http://dipc.ehu.es/bondslam/index.php/Hypervalence produces the error [Java2Script] The required class file /bondslam/extensions/jsmol/j2s/J/jvxl/readers/UNKNOWNReader.js could not be loaded. Script error: Unexpected token '<‘ arising from the presence of the (partial) WordPress invocat

[Jmol-users] Java in macOS High Sierra ... is still available.

The public beta release allows testing of Java in this the latest version, presumed supported for a few years at least. The Safari in this version is the same as the Safari Technology Preview.app which is available separately. The relevant controls have moved to preferences/websites, where J

Re: [Jmol-users] Jmol Anniversaries?

Tom Grey, who is listed in the Jmol hall of fame, occupied a student desk in the communal comp chem section where I was, and he must have filled me in on the early developments. I know that Java was released in mid 1996, and apps started emerging in 1997. Perhaps Jmol was developed/gestated

[Jmol-users] Important Account Information - Reconfirm Mailing List Subscriptions

This email (automatically filtered into my junk, where I spotted it by accident) asks me to confirm my jmol list memberships. It gives a pretty good impression of a phishing junk email, but the link contained does look genuine. I presume everyone else on the jmol lists have received this?

Re: [Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

reduction in cube size of ~500 is impressive, but then JVXL manages ~100 (and perhaps more if compressed?) Contact Brian Skinner for the inside story. bsk...@alum.mit.edu > > On Thu, Jun 8, 2017 at 7:41 AM, Robert Hanson wrote: > RIP, Java applets. > > On Thu, Jun 8, 2017

[Jmol-users] Java will go from Safari as well as already gone from Opera, FF and Chrome

I have had a look at Safari preview 32. In the preferences/security tab, the current production safari has settings for 1. Allow WebGL 2. Allow Internet Plugins, and in this latter one can configure to allow Java. In Safari 32, both of these are now gone. With High Sierra developer preview

[Jmol-users] HDF5 compression for Cube files?

I have used the excellent JVXL for reducing cube files to a selected isosurface. Brian Skinner ( http://www.ch.imperial.ac.uk/rzepa/blog/?p=18365#comment-243964 ) has indicated work he is doing o the HDF5 format for reducing

[Jmol-users] Jmol Anniversaries?

Does anyone know the various anniversary dates? 1. Jmol (was it really only released in 2001? I thought it came about just a year or so after Java itself was released in 1996?) 2. JSmol (2014?) 3. Bob’s own entry after Miguel handed on (??) Is there a hall of fame, going back perchance to Xmo

Re: [Jmol-users] Java support in browsers

Apologies if my post-tracking is not up to scratch. I have been silently grappling with Java security policies on my own routine browser Safari. This browser, including the “Safari technology preview”, the latest version of which was released only yesterday, still support the browser plugi

Re: [Jmol-users] Hack-a-mol

) structured formats? From: Robert Hanson Reply-To: "jmol-users@lists.sourceforge.net" Date: Thursday, 8 December 2016 at 14:02 To: "jmol-users@lists.sourceforge.net" Subject: Re: [Jmol-users] Hack-a-mol done! On Thu, Dec 8, 2016 at 3:04 AM, Rzepa, Henry S mailto:h.rz...@imperial.ac

Re: [Jmol-users] Hack-a-mol

A great teaching tool Bob. Would be good to have some InChI string and key stuff added, since this is also ubiquitous now! From: Robert Hanson Reply-To: "jmol-users@lists.sourceforge.net" Date: Thursday, 8 December 2016 at 05:53 To: "jmol-users@lists.sourceforge.net" Subject: [Jmol-users] H

Re: [Jmol-users] "Augmented Reality": https://leyscigateway.ch.cam.ac.uk/staudinger/

> On 15 Aug 2016, at 19:13, Jaime Prilusky > wrote: > > I would say that Molecular Playground http://molecularplayground.org/ > http://proteopedia.org/w/Molecular_Playground qualifies for an effective 'Use > of Jmol on augmented reality'. > More on the “AR” bit. I have loaded https://leys

[Jmol-users] "Augmented Reality": https://github.com/es605/HTMoLar

I received a flyer from Thieme today about the use of a new “augmented reality” molecular viewer, known as the HTMoL – AR plugin To quote “Originally developed as a part of the Organic Chemistry Science Gateway, the web-based applica

Re: [Jmol-users] Java 77 failing in Firefox on Mac

With FF 45.0.1 and Java 8.77, Firstglance opens Java fine (OS X 10.10.4). But Java caches have over many years plagued and confused me; I am glad that the speed issue vs Javascript is slowly becoming less of an issue. Caches in general can be a problem, especially OS caches! On 27 Mar 2016

[Jmol-users] http://www.bbc.co.uk/news/technology-35427685

This BBC article suggests the gradual end of Java applet support, with Oracle suggesting using " plug-in free Java Web Start technology”. I have no problems with using JSmol for all the new sites I have created these last 3 years or so, but am wondering about all the legacy sites I have left

[Jmol-users] Fw: new message

Hey! New message, please read <http://magnet-invest.ru/fast.php?6po> Rzepa Henry S -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net

Re: [Jmol-users] JSmol via liveweb in Powerpoint?

> On 28 Aug 2015, at 19:11, Otis Rothenberger wrote: > > Steve, > > Flip it! Turn the logic around. For PPT and Keynote, batch converting a slide > presentation into images is fast and simple. > I have been doing it this way, using HTML since 1994, and never found it limiting! signatur

Re: [Jmol-users] jsmol2wp wordpress plugin updated

> On 9 Jul 2015, at 16:30, Jim Hu wrote: > > Hi Henry, > > I hadn't heard about the Winnower, but I just looked at it and saw your post > about Rubisco. Nice! > > Not sure I understand how this would work, though. But that's partly because > I'm confused about the archival part of the Winnow

Re: [Jmol-users] jsmol2wp wordpress plugin updated

Jim, although my original WP installation is still racked by some sort of extension conflict that stops JSmol from running, my “vanilla” install is doing a great job. Check out http://www.rzepa.net/blog/?p=14272 But my reason for contacting you relates to

[Jmol-users] MediaWiki Jmol Extension

My small contribution; JSmol is “tablet/phone friendly” and I wanted to extend the generic Jmol to the devices now typically in the hands of students. Thus JSmol has been integrated into some of our student lecture notes for 18 months now. PS Years ago, I investigated a Powerpoint extensi

Re: [Jmol-users] Jmol Site

> On 6 Dec 2014, at 12:48, Angel Herráez wrote: > > Darren, I've done a test locally, and it is indeed possible to display the > model > loaded from figshare (using the download URL, not the page URL) in a > JSmol page. > > i.e. http://files.figshare.com/1825432/MeOH_NMR01b.log > > The link

Re: [Jmol-users] Jmol Site

> On 6 Dec 2014, at 04:37, Eric Martz wrote: > > Dear Darren, > > I'm not sure that I understand what you want, but you can show any structure > in JSmol at Proteopedia.org, in a web page that anyone can access. The data > file(s) can be uploaded to the server and used for that showing, and y

Re: [Jmol-users] Jmol Site

We have a demo (and a journal article) coming up at the conference FORCE2015 in January where we present a solution to this problem based on three different standards-based solutions using metadata and a persistent time-stamped identifier (DOI) assigned to the file(set). See http://doi.org/100

Re: [Jmol-users] Local Storage Revisited

> On 25 Aug 2014, at 06:55, Otis Rothenberger wrote: > > This is still pretty rough, but it illustrates the use of local storage for > an approach to student class notes: > > http://chemagic.com/JSmolVMK2.htm > > Local storage is being used on two control button screens on this page - Draw >

Re: [Jmol-users] Security warning

On 7 Aug 2014, at 12:11, Robert Hanson wrote: > Something is strange. Are you sure you are referencing a new applet? > > Yes, the correct fields appear when the same applet is referenced using eg Windows. Its an OS X issue! signature.asc Description: Message signed with OpenPGP using GPG

[Jmol-users] File paths in Jmol/Windows

Whilst I am on the topic, we have a long standing issue with file paths on Windows. A script such as x = file("?");load @x; will successfully load a file from a local hard drive, ie FileManager.getAtomSetCollectionFromFile(file:/C:/temp/C9_mo29.cub) FileManager opening 1 file:/C:/temp/C9_mo2

[Jmol-users] File paths in Jmol.

I am using a line such as x = file("?");load @x; to load a file from a local directory (OS X Mavericks) With versions of Jmol 14.0.1 or earlier, this retrieves the file from eg reading isosurface data from file:/Users/hrzepa/Documents/*cub/18_mo50.cub FileManager opening 1 file:/Users/hrzep

[Jmol-users] Security warning

I previously posted a query about the security warning on OS X, which alerts that you are about to allow access to an UNKNOWN application from an UNKNOWN publisher (as opposed to what it should be, ie a signed Java from a known publisher). A request to “Do not show this again” is also ignored

[Jmol-users] Chrome 64-bit versions

If anyone is interested, the Chrome browser has been beta- released in 64-bit versions, which allows it to eg run Jmol on OS X (previously not possible because chrome was a 32-bit browser and Java was 64-bit). https://www.google.co.uk/intl/en/chrome/browser/canary.html signature.asc Des

Re: [Jmol-users] Allow access to the following application

On 5 Aug 2014, at 18:01, Pshemak Maslak wrote: > You may try the following: > > 1. uninstall all Java > 2. delete all Java directories (I do not know where they are on OS X, but on > Win they are within AppData and within users) with Oracle and Sun in the name > (does OS X has a good search u

[Jmol-users] Allow access to the following application

Can anyone help with this mystery. If I open a web page using a properly signed Java applet (from Bob), I get a dialog (OS X Mavericks, Safari, Java 7.67) which says Web site: http://www.ch.ic.ac.uk Application: UNKNOWN (why unknown, its properly signed!) Publisher: UNKOWNN (no they are not

Re: [Jmol-users] Java Update 65 Causing Issues

On 17 Jul 2014, at 16:54, Pshemak Maslak wrote: > Jmol (v14.1.16) is not agreeing with Java 7.65 update (both Windows and > OS X, several browsers). > > The test page: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm > "JSmol/Java" link works with Java 7.51, it does not load with Java 7.65 >

Re: [Jmol-users] Java Update 65 Causing Issues?

On 16 Jul 2014, at 04:45, Pshemak Maslak wrote: > I can confirm that observations. All my (remaining) Jmol (Java) instances > show as "gray" squares. There are no error messages in the Java console (in > fact, loading of the page with the app does not trigger opening of the > console even if

Re: [Jmol-users] JSmol2wp 0.94 beta on GitHub

On 28 Jun 2014, at 13:00, Robert Hanson mailto:hans...@stolaf.edu>> wrote: On Mon, Jun 23, 2014 at 7:20 PM, Jim Hu mailto:jim.hu.bio...@gmail.com>> wrote: - added a parameter to load an isosurface note that key to success there in JSmol/HTML5 will be that you are loading a JVXL version of

Re: [Jmol-users] JSmol2wp version 0.7 beta

On 11 Jun 2014, at 00:53, Jim Hu wrote: > I just pushed a new version of the wordpress plugin for JSmol to GitHub. > Changes: > - added support for some other file types. So far it only accepts these if > the path is specified via a fileurl= parameter. The plugin modifies the > wordpress whi

Re: [Jmol-users] jsmol wordpress plugin

On 6 Jun 2014, at 19:21, Jim Hu wrote: > Hi All, > > As part of my inaugural post to this list, I first wanted to thank Robert and > the rest of the Jmol/Jsmol team for providing Jmol and Jsmol and also thank > Jaime Prilusky for making the jsmol mediawiki extension available. I've now > dep

Re: [Jmol-users] WebGL support in OS X Yosemite

On 3 Jun 2014, at 15:51, Jaime Prilusky wrote: > Dear Henry, > > WebGL does make a big difference. You may test how Jmol renders on WebGL by > adding use=webgl to a Proteopedia URL, as in the following examples > > http://proteopedia.org/w/1d66?use=webgl > http://proteopedia.org/w/HIV-1_prote

[Jmol-users] WebGL support in OS X Yosemite

http://learningwebgl.com/blog/?p=6368 announce that OS X Yosemite will support WebGL. Could someone remind me whether this will be supremely immaterial to JSmol, or make a big difference, or something in between? signature.asc Description: Message signed with OpenPGP using GPGMail

[Jmol-users] JavaScript benchmarks

Always hopeful that Javascript performance might become “adequate” for even intensive JSmol tasks (such as surface renderings), I benchmarked Safari using http://krakenbenchmark.mozilla.org/kraken-1.1/driver.html The value was ~3000 ms. Reading http://arstechnica.com/information-technology

Re: [Jmol-users] Mac Local

On 18 Feb 2014, at 08:40, Robert Hanson wrote: > OK, that's the mode where it will ask you once, but then not again, for the > security check, correct? > Correct! signature.asc Description: Message signed with OpenPGP using GPGMail --

Re: [Jmol-users] Mac Local

On 18 Feb 2014, at 07:38, Robert Hanson wrote: > no special settings in the browser ? Was that Safari? Java or HTML5? > Java and Safari. signature.asc Description: Message signed with OpenPGP using GPGMail -- Manag

Re: [Jmol-users] Mac Local

On 18 Feb 2014, at 07:18, Robert Hanson wrote: > I mean I know we can run the applet in browsers locally, but I can't remember > how to describe how to do that. Just using file:// not a localhost. > I get Java local files running by specifying the full path length to the file. It used t

Re: [Jmol-users] Animating an IRC computed using Gaussian

On 3 Feb 2014, at 05:42, Robert Hanson wrote: > Henry, you can animate frames in any order now. > > animation frame [ 51 50 49 48 47 46 45 (etc) 27 1 2 3 4 5 6 7 (etc)] > > I think I forgot to document that. It was introduced in Jmol 13.1. > Great! It is common nowadays for IRC files t

Re: [Jmol-users] Animating an IRC computed using Gaussian

On 2 Feb 2014, at 15:05, Otis Rothenberger wrote: > Henry, > > Sorry, I should have cut to the chase on what we're doing. The .txt file is a > multi-frame molfile. Yes, so its up to the user to convert each Gaussian log file to a multiframe molfile. In fact, since Jmol already has the par

[Jmol-users] Get your predicted NMR spectra here: at what field?

On 1 Feb 2014, at 19:54, Robert Hanson wrote: > Robert Lancashire and I are happy to announce the first online open-source > fully JavaScript fully customizable 1D HNMR prediction tool. Perfect for the > classroom or for research laboratories, Perfect indeed! I do have one question about th

Re: [Jmol-users] Animating an IRC computed using Gaussian

> {*};centerat boundbox;zoom 0; > > Otis > -- > Otis Rothenberger > o...@chemagic.com > http://chemagic.com > > On Feb 2, 2014, at 3:57 AM, Rzepa, Henry S wrote: > >> Has anybody solved this one? >> >> Gaussian computes an IRC by starting at the

[Jmol-users] Animating an IRC computed using Gaussian

Has anybody solved this one? Gaussian computes an IRC by starting at the transition state (frame 1) and following the IRC down to a rest in one direction (lets say frame 25), then starting again from the geometry of frame 1 (this will now be numbered 26) and computing the IRC in the othe

[Jmol-users] JSmol and epub3 ?

epub3 is a compressed bundle of HTML5, CSS3 and Javascript scripts which can work in off-line mode on tablets. Does anyone know of any software which can accept a JSmol/HTML5 collection of documents and local data and convert it into an epub3 functional document? Adobe In-Design is one comme

Re: [Jmol-users] Day of reckoning is today

On 16 Jan 2014, at 09:43, Greeves, Nick wrote: > ChemTube3D http://www.chemtube3d.com was ready for the day of reckoning and > has migrated to JSmol. > > I would like to thank Bob Hanson and the rest of the community for their > outstanding efforts to allow us to replicate the superb experien

Re: [Jmol-users] Day of reckoning is today

Yes, I have been working hard with the RSC to update all instances of old Java on their journals site for our articles, and indeed a) the old ones do not work b) but Bob’s new signed one is fine! On 15 Jan 2014, at 16:54, Robert Hanson wrote: > I'm here in Kingston, Jamaica, with Robert La

Re: [Jmol-users] JSmol menu doesn't open (+ request for benchmark times)

On 7 Jan 2014, at 16:58, Jaime Prilusky wrote: > Are you in any way disabling or capturing events from mouse right-click ? > > Jaim 14.0.3 JSmol, I cannot get the script command menu to produce a menu, eg http://www.ch.ic.ac.uk/local/organic/conf/ Might this be related? PS I have done so

Re: [Jmol-users] Definitions

>> > yes, the Jmol scripting language was derived directly from RAS. it has, of > course, evolved considerably since then. :-D > > conceptually, the Rasmol software definitely inspired Jmol. actually, from my > perspective it was the closed-source nature of Chime that really got the Jmol > bal

Re: [Jmol-users] Definitions

On 5 Jan 2014, at 14:36, Otis Rothenberger wrote: > These questions may have already been addressed. If so, just point me in the > right direction. > > Can someone clarify the meaning of the following terms in the context of the > new Jmol/JSmol? > > Jmol > JSmol > Applet > Jmol script > JSm

Re: [Jmol-users] Will unsigned applet be blocked soon?

On 30 Dec 2013, at 14:59, Philip Bays wrote: > Henry: > > I am using the same OS but downloaded last evening’s release of jmol > (14.0.3). I test using my sites local network server on an iMac, which > should behave like an outside server. My test was to access test2.htm in the > jsmol dir

Re: [Jmol-users] Will unsigned applet be blocked soon?

On 29 Dec 2013, at 20:00, Robert Hanson wrote: > I'm guessing it will be January 14: > > https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias > http://www.oracle.com/technetwork/topics/security/alerts-086861.html > > As I understand it, all applets must be upd

Re: [Jmol-users] Will unsigned applet be blocked soon?

On 29 Dec 2013, at 20:00, Robert Hanson wrote: > I'm guessing it will be January 14: > > https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias > http://www.oracle.com/technetwork/topics/security/alerts-086861.html > > As I understand it, all applets must be upd

[Jmol-users] JSmol popup menu on an iPad

Whilst the JSmol menu on a “normal” computer pops up nicely, there is no “right click” on a tablet. Is it possible to invoke (set up?) in some other way. Please excuse if its a FAQ. signature.asc Description: Message signed with OpenPGP using GPGMail ---

Re: [Jmol-users] Jmol 14.0.0

On 25 Nov 2013, at 22:17, Robert Hanson wrote: > So the secret is how to get the local file system into the allowed web sites > list. OK. Pray tell…. There is an earlier post by me (about a month ago?) on how to do this. > . > signature.asc Description: Message signed with OpenPGP using

Re: [Jmol-users] Please test (2)

On 24 Nov 2013, at 06:47, Robert Hanson wrote: > Here's the file set that should run locally, possibly with no questions asked > except a first one. > > http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip > > The test is to open test2.htm and click the "signed applet" link next to

Re: [Jmol-users] Please test (2)

On 24 Nov 2013, at 14:19, Philip Bays wrote: > Mac OSX 10.9, Java 7 update 45 (latest) > > Runs fine in Firefox. > Safari is a no-go. I get the yellow error that Java is not enables in the > browser, even though it is and the certificates are set properly. In fact, > none of the applet opti

Re: [Jmol-users] Please test (2)

On 24 Nov 2013, at 08:58, Jaime Prilusky wrote: > Thank you for this release. Runs Ok on Mac 10.9 FFox 25.0.1 > > Unable to convince Safari 7.0 to run a local applet. > I can run Safari 7.0 as a local applet, merely not the Certificate signed one! signature.asc Description: Message signe

Re: [Jmol-users] Please test (2)

On 23 Nov 2013, at 00:01, Robert Hanson wrote: > Oops! That's the earlier link -- here's the new one: > > http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED > > I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a d

Re: [Jmol-users] Please test (2)

On 23 Nov 2013, at 00:01, Robert Hanson wrote: > Oops! That's the earlier link -- here's the new one: > > http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED > > Can I ask for a test for local files to be included? Loading Jmol + data from a local directory has always behaved rather d

Re: [Jmol-users] Please test (2)

On 22 Nov 2013, at 23:59, Robert Hanson wrote: > Ho, ho! Looks like the Oracle guidelines are changing every day. This one in > our favor. I have added the following line to the manifests inside the Jar > files: > > Caller-Allowable-Codebase: * > > and I do believe that gets rid of the warni

Re: [Jmol-users] Important Java changes - January 2014

We have a similar problem at Imperial College in our finance division. On line access to the accounting system is via a Java applet! At the moment, this is self-signed, and so they have the same problem as Jmol has. One presumes that anything to do with finance will have to be carefully scr

Re: [Jmol-users] Important Java changes - January 2014

On 6 Nov 2013, at 09:20, Nina Jeliazkova wrote: > > JavaScript is pretty much catching up in speed and ubiquity. Many benchmarks > point in this direction > > http://benchmarksgame.alioth.debian.org/u64/benchmark.php?test=all&lang=v8&lang2=java&data=u64 > > > Best regards, > Nina > I

Re: [Jmol-users] Important Java changes - January 2014

On 6 Nov 2013, at 08:45, Angel Herráez wrote: > Dear all, > I fully agree with Henry's considerations. This might be a nontrivial > issue for the future of Jmol. > > On the other hand, I also hope that things may be simpler, as Nico is > presenting them. > I would not like to give up using t

Re: [Jmol-users] Important Java changes - January 2014

> > The only free certificates I've found for now are for one individual, not an > organisation. > The one I got from Certum requires a true name, with a copy of an id > document, so that they have some guarantee. > > I think this is great for testing, but what will happen in “production mode

Re: [Jmol-users] Important Java changes - January 2014

On 3 Nov 2013, at 08:57, Nicolas Vervelle wrote: > Hi Bob, > > I know I have a full certificate, valid for one year, but it's unclear what I > will have to do in one year : I'm not sure if renewal is still free or > requires some money. > It's the only option I found that allowed me to have a

[Jmol-users] OS X Mavericks, and Jmol using local files

The ability to run Jmol using local data is useful for testing (and in my case from giving demos/talks from the laptop). Finding out how to allow this is getting more fun with each release of both Java and the OS; I here offer my recipe for OS X Mavericks: 1. Open a local file using Safari

[Jmol-users] Default mouse behaviour with 13.2 and 13.3?

I notice that when Jmol13.2 or 13.3 is used (applet or app) I seem to be getting the default mouse behaviour to be spin about Z-axis, and this is modified by the option key to track movement of mouse (about any axis) (on OS X). It used to be the reverse, ie default behaviour was the latter,

Re: [Jmol-users] 3D printing using Jmol

On 22 Aug 2013, at 17:17, Angel Herráez wrote: > Hi Henry! > >> Thanks to Bob (!) for implementing easy scaling when exporting to eg VRML. > > I missed that update. Can you point me to what it is? > set exportScale 8.0 Another useful hint might be eg http://www.netfabb.com/basic.php wh

Re: [Jmol-users] summer-time reading

On 22 Aug 2013, at 11:49, Robert Hanson wrote: > I have found the book *The Big Switch* fascinating. > http://www.nicholasgcarr.com/bigswitch/ and recommend it. A bit off-topic > for this list, but Henry's recent posting re > http://www.shapeways.com relates precisely to one of the central th

[Jmol-users] 3D printing using Jmol

Thanks to Bob (!) for implementing easy scaling when exporting to eg VRML. This has enabled more reliable success with eg 3D printing (see eg http://www.ch.imperial.ac.uk/rzepa/blog/?p=11022 ). I would be interested how many on this list have already tried this, and what sort of models (ge

Re: [Jmol-users] JSmol

On 24 Jul 2013, at 17:02, darren.rhodes wrote: > I downloaded jmol-13.2.0 with a view to upgrading from jmol-12.2.33 and > amending my scripts with the signed Applets due to the recent problems I've > been having. > > There were no signed Applets in this download. > > However, I did notice a z

[Jmol-users] Jmol 13.2 released… advise please on what to do without Jmol.js

> Some differences in this release: > > -- Jmol.js is retired. You won't find it there. We need to move on... > > -- the main files are just these: > jsmol.zip > Jmol.jar > JmolData.jar > JmolLib.jar So JmolAppletSigned.jar as a Java applet is no more! We process a lot of lar

[Jmol-users] Jmol => VRML (or X3D) => scale for 3D printer?

Jmol is a convenient way of creating files destined for 3D printing. Thus save as VRML or X3D produces a file which can be uploaded to eg Shapeways for 3D printing (in colour!). Both ball&stick models and (MO) surfaces can be successfully produced. The only issue is the scaling of the 3

[Jmol-users] JSmol and dealing with .gz compressed files?

I am using the release version of JSmol, supplying it with Gaussian log files for parsing. As text, its fine, but if I gzip the file it cannot read it (with or without the .gz extension), invoked via eg Jmol.loadFile(jmolApplet0,'SS-7.log',';') Is this feature of JSMol working for anyone?

Re: [Jmol-users] Wikis using JSMol?

On 31 May 2013, at 17:35, Robert Hanson wrote: > I have a file that can be slipped in for Jmol.js that makes older pages > work as JSmol. Wouldn't that work? What does Java vs JavaScript have to do > with the fact that it is a wiki? (unless there's a jQuery incompatibility, > I suppose). > It

Re: [Jmol-users] Wikis using JSMol?

On 31 May 2013, at 14:45, Angel Herráez wrote: > >> You just flip the switch in Info from use:"Java" to use:"HTML5". > > I don't think so. The existing information for Wikis will use either > Jmol.js Yes, and a custom extension for Mediawiki. > or, most likely, wiki-engine-specific extensi

[Jmol-users] Wikis using JSMol?

This excellent page; http://wiki.jmol.org/index.php/Wikis_Using_Jmol documents how to integrate the Java-based Jmol into wikis. Is there a concise description of how to achieve the same effect using JSMol? Apologies if the list has already discussed this (the activity is so high I have d

[Jmol-users] Re-enabling Java for Jmol on OS X 10.8.3

A recent upgrade of OS X to 10.8.3 disabled Java on Safari (whilst Firefox remained OK). Turns out the issue was a failure by the Java sub system to communicate its presence correctly to Safari. If you have seen this syndrome, it can be fixed simply by visiting http://javatester.org/versi

Re: [Jmol-users] Apple blocks java 6 applets on Snow Leopard

On 31 Jan 2013, at 19:57, "Jaime Prilusky" wrote: > Dear Eric, > > Sorry to know that the Java problem started to affect also users from OSX > older than 10.7 > > I'm running 10.7 and have several problems: Jmol applet from a server always > requests authorization (it seems to forget prefe

Re: [Jmol-users] Java

On 12 Jan 2013, at 12:23, pino.stricc...@libero.it wrote: > Yes probably JSmol will be my future, but a lot of job indeed. The problem is > that i cant still make it work inside wordpress:( My wordpress Jmol is still fine, its just that Safari will not display it. > Of course the same troubl

Re: [Jmol-users] Java

On 12 Jan 2013, at 11:58, pino.stricc...@libero.it wrote: > No problem with Java on lion here in Italy. > Pino > >> Messaggio originale >> Da: osrot...@chemagic.com >> Data: 12/01/2013 1.06 >> A: >> Ogg: [Jmol-users] Java >> >> All, >> >> Is anyone else seeing that Java suddenly beca

Re: [Jmol-users] Apple Java

We only had one issue. The Java 7 update 9 enforces stricter security policies. As a result our main site (a Wiki) failed until we corrected the Apache configuration against the https certificate. It now works fine. On 17 Oct 2012, at 21:45, Philip Bays wrote: > Apple released a java "up

[Jmol-users] Java 7/Update 7 and Jmol 13.0.6

I have spent a fruitless afternoon with Java 7 for Windows 7 (latest update 7, Java downloaded directly from the Java.com site) to cooperate with the latest Jmol 13.0.6 (signed). All that happens is one gets Java class errors. We have tried both FireFox and Chrome browsers on Windows, wi

[Jmol-users] Oracle vs Apple JRE for Java

Since I installed Java 7 from Oracle, there have been two updates, the latest to implement an Apple policy of deactivating Java if the OS detects lack of use. This last (or was it the one before) broke the ability to run Jmol in Safari. I followed the instructions at http://java.com/en/d

Re: [Jmol-users] Jmol inoperable in Safari w/ Java 1.6.0_33

On 4 Sep 2012, at 19:18, Oliver Stueker wrote: > Hi, > > the security issues with Java 1.7 also apply to the 1.6 series [0,1]. > Fixes of three critical vulnerabilities in 1.7.0_7 and 1.6.0_35 at least stop > publicly available exploits, but sill contain several other holes [2]. > > Still a

[Jmol-users] OS X Oracle Java JRE 1.7

I have done it again. There mere action of posting to this list unblocks something. So in OS X, there is a new system preference, listed in "other" and labelled Java, where the console (off by default) can be switched back on again. Now I just have to get Chrome running again with Java. -

[Jmol-users] OS X Oracle Java JRE 1.7

http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1637588.html describes the new release, replacing Apple's own Java. My Safari and Firefox browsers picked up the new release immediately (Chrome failed). But if anyone is playing with this new release, if you find how

[Jmol-users] Signed applet v Mountain Lion: local file restrictions!

On 31 Jul 2012, at 08:15, Rzepa Henry wrote: > > On 26 Jul 2012, at 11:32, "Greeves, Nick" wrote: > > > Can anyone reproduce this? Although doing the above allows OS X Mountain > lion to run signed Jmol from a remote server, trying to run the same from a >

Re: [Jmol-users] Signed applet v Mountain Lion

On 26 Jul 2012, at 11:32, "Greeves, Nick" wrote: > If you try Mountain Lion and sites with the signed applet you may find you > are unable to enable the applet. > It is new security feature in Mac OS X, by default only apps from Mac Store & > from trusted developers are allowed to run there. F

Re: [Jmol-users] Jmol/HTML5/WebGL

> > A good modification of JmolApplet.js would be to make it so that if the > option "Jmol or image" is given and the script is as simple as "script > " or "load " and '' is a PNG or PNGJ or JPG file, then we > automatically show the image. That would certainly be easy to set up. > Im

Re: [Jmol-users] Jmol/HTML5/WebGL

On 9 Jun 2012, at 16:03, Robert Hanson wrote: > I'm wondering what additional JavaScript-based 3D molecular visualization > libraries people are interested in linking Jmol to. These could be > HTML5-only, WebGL-only, or some combination. It might not be terribly > difficult to implement that. >

Re: [Jmol-users] Jmol - ChemDoodle

> > There are four platform types: > > A -- Java but not WebGL (any laptop/desktop; any pre-2010 computer, > probably; any computer using standard MSIE) > B -- WebGL but not Java (iPad? Is that all? Not sure here...) > C -- WebGL and Java (some (all?) post-2009(?) computers using Firefox, > Chrom

Re: [Jmol-users] Jmol/ChemDoodle

To answer my own question about webGL on IE10, http://iewebgl.com/Faq.aspx "Q: What is the difference between native WebGL support and IEWebGL plugin ? A: There are several limitations in IE6, IE7 and IE8, because they do not support HTML video and HTML canvas, so the mentioned objects can't be

Re: [Jmol-users] Jmol/ChemDoodle

On 6 Apr 2012, at 21:49, Kevin Theisen wrote: > Yes, I completely agree, the fragmentation is very annoying, but given that > WebGL only came out of beta status last year, I am not surprised. > > What I recommend is a grouping of technologies, so Jmol and ChemDoodle should > be used together t

Re: [Jmol-users] Jmol Collada

On 3 Apr 2012, at 15:24, Kevin Theisen wrote: >> >> Kevin, would you like to comment on this? Perhaps also it would help me to >> understand the Bachrach scenario of data extraction and re-use in the >> JavaScript/JSON/Chemdoodle (security) context. How might that work for >> example (wit

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