Re: [Jmol-users] getting the applet ID

It’s probably not recommended, but this may do the trick Object.keys(Jmol._applets) ? Paul > Le 29-06-2017 à 14:58, Angel Herráez a écrit : > > Callbacks return as their first parameter the ID of the JSmol object (e.g. > "jmolApplet1") > > I wonder if this ID could be

Re: [Jmol-users] Jmol Anniversaries?

Hi, digging in sourceforge jmol-developers list, I found that Bob starts appearing as a recurring character in 2005 and secures the leading role in developping Jmol in mid 2006 after having exhausted Miguel with thousands of messages and commits. That was around Jmol v10.x It looks like we

Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

crit : > > And don't forget that Jmol has a WebGL option, but I don't claim that it is > any better than the others. It's not our forte, and it comes with a > significant overhead if all you want is a molecule to show. > > On Tue, Nov 3, 2015 at 1:57 PM, Paul PILLOT <paulpil..

Re: [Jmol-users] how to parse JSON data within Jmol

Le 13-01-2016 à 20:58, Paul PILLOT <paulpil...@gmail.com> a écrit : Hi Eric, rcsb implements a REST API that you can query through Ajax to get many answers to a lot of question. Here is an example of code I designed to get informations from a PDB, such as the number and names of

Re: [Jmol-users] labels and zshade

edu> a écrit : > > I believe that is the design. Otherwise labels would be faded out and > probably hard to read anyway. > > On Mon, Jan 4, 2016 at 8:45 PM, Paul PILLOT <paulpil...@gmail.com > <mailto:paulpil...@gmail.com>> wrote: > Dear Jmolers, > I d

[Jmol-users] labels and zshade

Dear Jmolers, I don’t know if this is a recent change, but I’ve just realized with Jsmol latest version that when zshade is on, labels of atoms located behind the mid plane are hidden. Is there a way to switch off this behaviour ? -Paul

Re: [Jmol-users] test please

I’ve made quick tests in Safari console. array.slice() works Int32Array.slice doesn’t work, but ArrayBuffer.slice from the same typed array works. Paul > Le 21-12-2015 à 17:03, Robert Hanson a écrit : > > Thanks, that's what I needed to know. Looks like "array.slice" or at

Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

Regarding strings, from what I experienced, getting a value from an array is a lot faster when the array is index based than when the array is associative (strings as indexes) Don’t know if that applies to your case... Paul > Le 18-12-2015 à 15:15, Robert Hanson a écrit : >

Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

According to jsperf ( https://jsperf.com/string-concatenation/106 ) your syntax seems optimal. > Le 18-12-2015 à 15:30, Robert Hanson a écrit : > > I was thinking of alternatives to > > s = "a" + "b" + "c" > >

Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

Hi Rolf, my experience in this area is not JSmol related, but when I had to deal with big tables in javascript (for a multiple sequence alignment script, aligning 2 sequences of 5000 signs, requires at least 1 table of 5000 rows and 5000 columns), I noticed that : - using integers only tables

Re: [Jmol-users] Fwd: Chrome: rotation unusable in JSmol

Dear Eric, I’ve noticed the same problems, especially on older computers where each scene repaint can be perceived (white background flashing between each frame). One of my pages has other concerns related to javascript event listeners that make the whole experience even worse, by adding other

Re: [Jmol-users] draw curved arrows

Angel & Killian, "set hermitelevel 7" would be more appropriate when using povray for an output (antialias doesn’t change the geometries in the pov file) Paul > Le 16-11-2015 à 12:14, Angel Herráez a écrit : > > Hi Kilian > > I'm afraid the succession of spheres is

Re: [Jmol-users] set picking rotate bond broken ?

Otis, what Bob means is that the command « set picking rotatebond » by itself is not broken. But it requires a key modifier + mouse drag combination to work. What I did on my webpage (thanks to the code I saw on yours) is to as a bind command as previously explained, so that no key modifier is

Re: [Jmol-users] set picking rotate bond broken ?

rger > o...@chemagic.com > http://chemagic.com > >> On Nov 11, 2015, at 10:03 PM, Paul PILLOT <paulpil...@gmail.com> wrote: >> >> Thanks Otis ! >> your answer pointed me to a description of the gesture I was looking for : >> MAJ+Left_click >>

Re: [Jmol-users] set picking rotate bond broken ?

> using the bind command to bind to a specific mouse/key action? > > Otis > > Sent from my iPad > >> On Nov 11, 2015, at 8:06 PM, Paul PILLOT <paulpil...@gmail.com> wrote: >> >> Hi, >> I am wondering if the « set picking rotatebond » command is bro

[Jmol-users] set picking rotate bond broken ?

Hi, I am wondering if the « set picking rotatebond » command is broken ? I’ve tried bot with the application (v 14.5.0_2015.11.06) and the HTML5 jsmol flavour Bonds are selected by picking, but I can’t rotate any group from either side of the bond. Am I missing something (key modifier for

Re: [Jmol-users] Request for help: Outlines for atoms (and bonds)

halos mays also be an option http://chemapps.stolaf.edu/jmol/docs/#halos -Paul > Le 10-11-2015 à 14:35, Angel Herráez a écrit : > > Oh yes! > > Go to the documentation page, > http://chemapps.stolaf.edu/jmol/docs/ > and search for "outline" > and you have > set

Re: [Jmol-users] State of the world of WebGL "alternatives" to JSmol

Hi Angel, feel free to include this comparison in the wiki for further reference. I fully agree with all your comments. Persistency of web libraries is an important aspect. Some are funded projects (3Dmol.js relies on a grant), some are academic or backed by public institutions. Open source

Re: [Jmol-users] Showing CIF atoms at vertices of the cell

try « packed » Paul > Le 15-10-2015 à 14:30, Xavier Prat-Resina a écrit : > > Hello, > > I'm trying to display the unit cell of ZnS from a CIF file by using: > > load ZnS_blende.cif {1 1 1} > > See here: http://chemdata.r.umn.edu/jmol/blende.html >

Re: [Jmol-users] JSmol/HTML5 - Forced usage

Hi Rolf, the only way to override the info setting I know about is through the URL, by adding a flag : http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Setting_parameters_from_the_URL -Paul > Le 01-10-2015 à 10:37, Rolf Huehne a écrit : > > Hi all, > > is there a

Re: [Jmol-users] PubChem Widget

Hi Otis, this is a very impressive website, thank-you for the link. I’ve found the documentation for the Pubchem autocomplete widget : https://pubchem.ncbi.nlm.nih.gov/widget/docs/widget_autocomplete_help.html -Paul >

Re: [Jmol-users] try again

You’re right : jsmol.htm indeed works like a charm ! Paul > Le 16-09-2015 à 09:16, J. Bays a écrit : > > Paul: I think that is intentional. Try jsmol.htm. It is the same test without > > J. Philip Bays > Emeritus Professor of Chemistry > Saint Mary's Collegethe images.

Re: [Jmol-users] try again

Everything works as expected (including localization alerts, filter2D, fractional coordinates shorthand notation) ! Thanks a lot Bob ! The only remaining glitch is in the test2.htm page that displays 2 still images in the forefront, having the active molecule displayed ind the background. It

Re: [Jmol-users] last release before Jmol 14.4, hopefully!

The language bug is still present (to test this, set up your browser language to another than english). -Paul > Le 14-09-2015 à 19:15, Robert Hanson a écrit : > >

Re: [Jmol-users] last release before Jmol 14.4, hopefully!

Here is the test : - I’ve downloaded jsmol (extracted from jmol-14.3.16_2015.09.14.zip) and copied the folder in a repository on my local Apache web server - from the browser (same results with Firefox, Safari and Chrome on Mac OS X 10.10.5), I run the test2.htm page - I get the 4 following

Re: [Jmol-users] Jmol -- testing requested -- load filter "2D" not working

0 > 1 2 1 0 0 0 > M END "model";calculate hydrogens;minimize > > Otis > > > > -- > Otis Rothenberger > o...@chemagic.com <mailto:o...@chemagic.com> > http://chemagic.com > >> On Sep 13, 2015, at 11:26 PM, Paul PILLOT <paul

[Jmol-users] Jmol -- testing requested -- load filter "2D" not working

Hi Jmolers, I’ve tried with the 2 latest versions of Jmol (14.3.16, 14.2.15) and they both seem broken in respect with this command. Test case : copy and paste the following in Jmol console : load DATA "model" Ethane http://www.ichemlabs.com 2 1 0 0 0 0999 v2000 -0.4330

Re: [Jmol-users] get {} value without knowing key?

print x[x.keys[3]] works, but there might exist a shorter way of doing this… -Paul Le 30-08-2015 à 20:49, Eric Martz ema...@microbio.umass.edu a écrit : load =1al4 x = {altloc!=}.altloc.all.pivot Now we have an associative array with key:value pairs: $ print x { A : 238 B :

Re: [Jmol-users] Jmol -- testing requested

Hi Bob, the 2 error messages on startup are displayed on MacOS X.10.5, Safari 8.0.8 TypeError: undefined is not an object (evaluating 'J.api.Interface.getInterface') try/catch path: 0 function (b, d) args[0]=TypeError: undefined is not an object (evaluating 'J.api.Int... args[1]=function ()

Re: [Jmol-users] Jmol -- testing requested

Thanks Otis, I am also running pages from my local web server (localhost). I haven’t spotted the setting you are referring to. I have made further tests with firefox 40 and Chrome 44. The three browsers give the same consistent error messages (that don’t prevent jsmol from working). Paul Le

Re: [Jmol-users] Jmol speed

Maybe because you’re mentioning it, it indeed looks faster. I’ve also tried the webGL demo and I am sorry to report that it’s broken http://chemapps.stolaf.edu/jmol/jsmol/jsmolgl.htm Paul Le 2 mars 2014 à 00:02, Robert Hanson hans...@stolaf.edu a écrit : Is it just my wishful thinking, or

Re: [Jmol-users] Question: What is the preferred way to save JSmol state and orientation?

Hi Chuck, have you tried « get property stateInfo » ? It should restore everything including orientation, zoom, etc… Paul Le 31 janv. 2014 à 16:32, Charles Harrison Shubert cshub...@mit.edu a écrit : Hi, When my users open my app, I'd like for JSmol to be in the same state that they left

[Jmol-users] JSmol HTML5 code : remaining /div

Hi, trying to debug one of my webpages that doesn’t display the HTML5 Jmol (without throwing any error) but that does display the Java version, I’ve looked at the generated code (jmolApplet0._code) and saw this for the canvas2D version : /divdiv id=jmolApplet0_2dappletdiv

Re: [Jmol-users] Safari test -- fixes Boolean issue?

It works ! Mac OSX.9 Safari Version 7.0 (9537.71) (the display is a lot slower than what I get with firefox) Paul Le 3 déc. 2013 à 13:54, Robert Hanson hans...@stolaf.edu a écrit : and http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm and http://chemapps.stolaf.edu/jmol/jsmol/simple2.htm

Re: [Jmol-users] local testing ready iteration 1,203,304,440

If you have access to your server’s feature, you can also enable gzip compression (on Apache it’s the mo_deflate program) for the associated plain text format. Then the server and the browser will do the job ! Paul Le 28 nov. 2013 à 13:12, Rolf Huehne rhue...@fli-leibniz.de a écrit : On

Re: [Jmol-users] How to set up a molecular playground

Dear Angel, thank-you for your answer. I've sent a message to Craig Martin, but he might be busy at the moment. I am also wondering at the scripts and the way they succeed from one to another. Bob mentions in the source code that he uses a simple Excel spreadsheet with 3 columns. I have found it

[Jmol-users] How to set up a molecular playground

Dear Jmolers, I would like to set up a Molecular playground. I have read extensively the molecularplayground.org website, but I could not find any information regarding the software used nor download it. After some googling, I've seen on Angel's dedicated webpage that MPControlHub and MPJmolApp

Re: [Jmol-users] Some Desirable Features!

I think it is possible through the javascript file api to get access to the content of a local file, and then send this content to Jsmol with the load data function. The drawback is that the file api is not well supported across all browsers, at least I've tried it successfully with firefox a

Re: [Jmol-users] JSmol too slow!

Try: Jmol.script(jmolAppletObjectNameComesHere,load =PDBID) where jmolAppletObjectNameComesHere is the name you gave to your jmol object instance at creation Paul Le 10 sept. 2013 à 18:01, Amjad Farooq a écrit : Bob, I checked out your new JSmol page with the protein loaded in at:

Re: [Jmol-users] jsmol issue

Not exactly the subject, but when downloading a pdb file from RCSB website, the server checks if the browser accepts compressions and compress the pdb file on the file. You don't have to explicitly request a pdb.gz file to get the benefits from data compression. Paul Le 8 sept. 2013 à 08:25,

Re: [Jmol-users] language localization for JSmol

It works great now ! Bravo ! Paul Le 22 mars 2013 à 03:08, Robert Hanson a écrit : OK, the Chrome business should be fixed. http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm On Thu, Mar 21, 2013 at 1:07 PM, Robert Hanson hans...@stolaf.edu wrote: OK, the problem with Chrome is that

Re: [Jmol-users] About adjustment of jmol applet window size by mouse

plus set antialiasdisplay true -Paul Le 20 mars 2013 à 19:46, Angel Herráez a écrit : But the cartoons structure of my test applet looks not very smooth and has jagged edges. I am wondering if there are any other features to get smoother structure. It may depend on your particular

Re: [Jmol-users] language localization for JSmol

The message is still in english for me Tested on OSX.6 Chrome Version 25.0.1364.172 in french after clearing the cache. -Paul Le 20 mars 2013 à 20:54, Robert Hanson a écrit : I've updated that after Angel's helpful tests. It should be working now:

Re: [Jmol-users] language localization for JSmol

2013) $ You could also enter this in the developer console: J.i18n.GT.getLanguage() or Jmol.featureDetection.getDefaultLanguage() Bob On Wed, Mar 20, 2013 at 3:07 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: The message is still in english for me Tested

[Jmol-users] WebGL version broken ?

Apparently the WebGL version is broken on test2.htm Chrome's console says : Uncaught TypeError: Cannot read property '_is2D' of undefined (JSmol.js:206) Paul -- Symantec Endpoint Protection 12 positioned as A LEADER in

Re: [Jmol-users] issues with converting to jsmol

works for me on OsX with Chrome : inline: Capture d’écran 2013-02-20 à 22.42.32.png -Paul Le 20 févr. 2013 à 22:24, Jennifer L. Muzyka a écrit : I'm working on converting pages from Jmol to JSmol and am seeing a strange and mysterious phenomenon, with the structures showing up in a different

Re: [Jmol-users] Problem with switching to JSMol

Order matters in your js files links I use the following declaration: script type=text/javascript src=jmol/JSmol.min.js/script script type=text/javascript src=jmol/j2s/j2sjmol.js/script That is with the minified version and without webGL. Paul Le 22 févr. 2013 à 12:43, Simone Sturniolo a écrit :

Re: [Jmol-users] Transfer show info from JSO to Javascript?

Jmol.evaluate(myJmol1,script(show orientation)) will do ! -Paul Le 22 févr. 2013 à 20:27, Dan Kirshner a écrit : Sorry, I'm just not getting how to do this. I'd like to get the quaternion info for the current model rotation and manipulate it in Javascript. I'm using the Jmol Javascript

Re: [Jmol-users] Signed applet, LoadInline and ajax/db

You can prevent eval() in your code with : document[applet_name].Loadinline(sdf) Paul Le 7 févr. 2013 à 17:42, Otis Rothenberger a écrit : Quentin, I'm not fully following your use of pipes, but I think one error is the following: sdf=sdf.replace(/\|/g,\n|); I think you need //n not

Re: [Jmol-users] JSmol lite

Minimified and Gzipped, Jsmol is a 700-800kB download. I am not sure that reducing the download is the way to go in order to improve user experience on mobile phones. I've seen JSmol once on an Iphone and it was really slow. Too slow to call it interactive. Maybe targeting at the graphic

Re: [Jmol-users] how do you align center?

Have you tried the css margin: 0 auto; ? Paul Le 28 janv. 2013 à 19:52, Jonathan Gough a écrit : I can embed a jsmol, using the script nomenclature, but I can't seem to align the embed to the center. I have tried using allign center and div classes, but nothing. any suggestions?

[Jmol-users] bug with signed applet, show history and Jmol.scriptWaitAsArray()

I am converting a former Jmol.js web page to the JOO script library and after some testings I've narrowed down the following bug : - when the signed applet is used and commands are sent with Jmol.scriptWaitAsArray(), the aforementioned commands are not displayed by the show history command -

Re: [Jmol-users] bug with signed applet, show history and Jmol.scriptWaitAsArray()

Thanks Bob ! I've made more tests using the signed applet on the test2.htm page and found the same problem : script sent via Jmol.scriptWait AsArray(jmolApplet0,...) are not added to the history, whereas scripts sent through Jmol.script(jmolApplet0,...) are. On the test page simple.html (that

Re: [Jmol-users] bug with signed applet, show history and Jmol.scriptWaitAsArray()

, Jan 27, 2013 at 4:24 PM, Robert Hanson hans...@stolaf.edu wrote: I should be able to track that down... On Sun, Jan 27, 2013 at 4:00 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: Thanks Bob ! I've made more tests using the signed applet on the test2.htm page and found the same

[Jmol-users] bug with Jmol.evaluate and script('show history')

to track that down... On Sun, Jan 27, 2013 at 4:00 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: Thanks Bob ! I've made more tests using the signed applet on the test2.htm page and found the same problem : script sent via Jmol.scriptWait AsArray(jmolApplet0,...) are not added

Re: [Jmol-users] bug with Jmol.evaluate and script('show history')

It's working ! Thanks Bob ! Le 27 janv. 2013 à 21:57, Robert Hanson a écrit : I see it. The show history command is supposed to clear out the show history command itself, but only if it is not a top-level command (from the console), but it does more than that if it is part of script(show

Re: [Jmol-users] Fwd: Jmol iPad app

I've been asked some time ago, about a facility aimed at students for combining a web textbook with the ability to interact with 3D models. The textbook could be something close to wikipedia, that is articles with links making it easy to jump to a glossary for example, or to scientific

Re: [Jmol-users] JSmol version issue

Otis, web inspector on safari have a panel to show this activity (network) : which files are indeed loaded, which others are loaded from cache you'll have a very informative timeline as well -Paul Le 16 janv. 2013 à 16:31, Otis Rothenberger a écrit : Phil, Still like clockwork - 40 seconds.

[Jmol-users] calculate partialcharge broken ?

Apparently the command calculate partialcharge doesn't work in v13.1.11 and causes the applet to stop working To reproduce the bug : http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm Click Load MOL by NAME Load the default model Type in the command slot : calculate partialcharge the

Re: [Jmol-users] gzip pdb file in JSmol

Hi, do you have a pointer to this file, so that we can have a look at the headers ? Does Safari on your Mac load this gzipped file well ? Paul Le 12 déc. 2012 à 19:02, Wayne Decatur a écrit : Hi, I have JSmol opening a gzipped pdb file served from a web server on a Mac. All is well there.

[Jmol-users] testing needed for xml loading

On Chrome MacOSX.6 no error with vasp.xml and water.xodydata. estron.cml reports the following error : FileManager.getAtomSetCollectionFromFile(estron.cml) starting HoverWatcher_7 FileManager opening http://chemapps.stolaf.edu/jmol/jsmol/estron.cml The Resolver thinks XmlCml call loadScript

Re: [Jmol-users] testing needed for xml loading

Rothenberger o...@chemagic.com http://chemagic.com On Dec 10, 2012, at 7:58 AM, Paul Pillot wrote: On Chrome MacOSX.6 no error with vasp.xml and water.xodydata. estron.cml reports the following error : FileManager.getAtomSetCollectionFromFile(estron.cml) starting HoverWatcher_7

Re: [Jmol-users] Ketcher

prototypejs defines a global $() object as well as jquery. ketcher relies on prototypejs and jsmol on jquery a conflict probably lies there -Paul Le 30 nov. 2012 à 16:30, Robert Hanson a écrit : It would be interesting to know more about those code collisions. We don't want to have to use

[Jmol-users] JSmol -- Are we done? Gestures

So many improvements, it's hard to keep pace. I've just (re)tried with an iPad and found out that gestures now work : pinch to zoom, two fingers for a translation. There is even a support for picking measurements through double tap. This is fabulous ! Measurements are tricky : it's difficult to

Re: [Jmol-users] minimization using GPU

Apparently WebCL is the technology involved here, but it is not supported yet natively by any browser. Extensions exist for firefox and webkit. -Paul Le 25 nov. 2012 à 18:05, Dan Damelin a écrit : Hi Bob, At the moment we don't have any free cycles in our development group for something

Re: [Jmol-users] JSmol -- Are we done?

The zip file available is apparently an older version (from the 11/13). There might be some caching problem there, preventing from downloading the latest version ? I don't know if it's time to discuss this yet, but I have some comments about JSmol: - speed performance: a colleague of mine

[Jmol-users] JSmol - three months in... and compression

I've tried minifying JSmol (yes, again), with the new version. After gziping by the server, the results are : - 720kB with WebGL - 666kB without WebGL (including 4kB just for the HTML page) (I don't have the extra download of 40+ files, as I had previously so the minifying process works as

Re: [Jmol-users] two JSmols in the page

Hi Angel, have you tried plain test2.htm first ? I encountered a problem with the zip distribution at some point yesterday and these error messages look familiar. Paul Le 20 nov. 2012 à 21:05, Angel Herráez a écrit : Dear all, I'm trying a page with two Jmols using Jmol-JSO. My code is like

Re: [Jmol-users] My trial wit JSmol

Le 16 nov. 2012 à 18:04, Robert Hanson a écrit : Ultimately, I think we will still end up with the full load of 600 or so .js files. I know that sounds ridiculous, but really what it means is that there are so many options in Jmol, that defining or implementing all of them at once

[Jmol-users] JSmol gz compression

I've enabled Apache mod-deflate on my local machine. It compresses all html/js/css files. I have also minimified, thanks to uglifyjs2, core.z.js (down to a 2.6MB file) Loading the test2.htm page on my local server resulted in a 2.9MB transfer, whereas the same page results in a 4.09MB transfer.

Re: [Jmol-users] JSmol gz compression

It works and caffeine is loaded after a 871kB download ! core.js is sent as a 564kB file. Surprisingly 43 js files are loaded after core.js (shaperenderer.js, ballrenderer.js, deflate.js, gzipheaders.js to name a few). Those files are not loaded on the test page delivered by the chemapps...

[Jmol-users] JSmol compression techniques

the httpd.conf file of my Apache server in accordance with this tutorial : http://www.techiepark.com/tutorials/how-to-enable-gzip-compression-in-apache-server-to-speed-up-website/ mol and pdb files also benefit from this setting Paul Le 19 nov. 2012 à 20:52, Paul Pillot a écrit : It works

Re: [Jmol-users] JSmol compression techniques

On Nov 19, 2012, at 3:51 PM, Robert Hanson hans...@stolaf.edu wrote: On Mon, Nov 19, 2012 at 3:41 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: So... by combining all the JSmol.js files (including the huge three.js library for webGL) in a minimified version, I got a 418kB

Re: [Jmol-users] JSmol tweaks

My mistake : variables names are changed to reduced ones (one letter), but this is not the case for objects names (such as Long, Clazz,... etc...) nor for their methods. Paul Le 18 nov. 2012 à 23:28, Paul Pillot a écrit : For information, I've just tried to minimify the jsmocore.z.js file

Re: [Jmol-users] JSmol tweaks

to know that this 1.6MB file can be gziped to a 500kB file. So, minimification + gzip compression could reduce the load by 7 (3.4MB0.5MB). Paul Le 18 nov. 2012 à 23:50, Paul Pillot a écrit : For information, I've just tried to minimify the jsmocore.z.js file using the uglifyjs library

Re: [Jmol-users] JSmol tweaks

Apparently, one can set up the server to choose which version of the file (gzip or plain) to deliver accordingly with the headers sent by the client's browser. Apache mod-gzip + caching seems to achieve similar results. Paul Le 19 nov. 2012 à 01:12, Evans, Michael James a écrit : Angel,

Re: [Jmol-users] JSmol advancements -- threads

Looks great ! Just for curiosity's sake, aren't web workers good alternative to threads in javascript ? Le 19 nov. 2012 à 03:17, Robert Hanson a écrit : OK, we have basically everything we had in Jmol in terms of threads -- tasks that run independently. It's a fake -- in a browser you get

[Jmol-users] JSmol and Jquery mobile

This might be of interest to some of this list users, I've tried to make a web app aimed at tablets or other mobile platforms using jsmol. I tried the Jquery mobile framework to achieve this, but I had a very strange result regarding the Jmol canvas : rotation was unavailable (click and drag

Re: [Jmol-users] Give this a try...

This is fabulous ! I've just tried it on my laptop and on an Ipad, it worked great on both ! This unveils a new continent of possibilities, thank-you Bob ! Loading takes a bit of time for the first run : my browser pulled 313 requests. I suspect it could also be speed up by compressing the js

Re: [Jmol-users] Creating multiple instances of JmolViewer

There is just one Jmol object, but you can have several applets. Maybe what you describe is due to trying no create several Jmol objects ? Paul Le 28 sept. 2012 à 16:52, Andreas Truszkowski a écrit : Hi Bob, it seams that the first instance is updated by the executed scripts of the second

Re: [Jmol-users] write command to server

Alex beat me to it. Right. Sorry, it's not the WRITE command. It's this: Var x = load(http://xxx.xxx.xxx/servlet/?POST?_PNGJBIN_;) You will get a return from your server, but in the process Jmol will send the PNGJ file in the POST. I can send you the PHP side of this if you want to

Re: [Jmol-users] Notify user if signed applet request is declined

Try jmolScriptWait() instead Paul Le 28 juin 2012 à 09:40, Martin Hediger a écrit : I tried show _signedApplet in the Jmol console, which nicely prints true. However, jmolScript('show _signedApplet') on the console of the browser returns undefined. On 27.06.12 15:19, Rolf

Re: [Jmol-users] Resolver Test Request

Tried it twice today (morning and afternoon): - first link has always worked - second link never worked on the first attempt, only on the second try -- Live Security Virtual Conference Exclusive live event will cover all

Re: [Jmol-users] Resolver Test Request

? Is it theoretically possible to hit Resolver directly via the JmolScript? Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jun 28, 2012, at 9:07 AM, Paul Pillot wrote: Tried it twice today (morning and afternoon): - first link has always worked - second link never worked

Re: [Jmol-users] Notify user if signed applet request is declined

With getproperty appletInfo, you can access the name of the applet : appletInfo.htmlName=jmolApplet0 From there, you can guess if it's signed or not... (haven't tried it but I suspect it should work) Paul Le 27 juin 2012 à 14:25, Martin Hediger a écrit : Just to be clear, I'm not reporting any

Re: [Jmol-users] Notify user if signed applet request is declined

Sorry, this doesn't work: the signed applet gives back the same name as the unsigned... Last thing I can think of is a try{} catch {} where you could try to load a dummy file from a different domain... Paul Le 27 juin 2012 à 14:47, Paul Pillot a écrit : With getproperty appletInfo, you can

Re: [Jmol-users] Question Jmol / CGI response

That's probably not related to the issue you reported, but this part of the js might have performance issues : function build_interface(resp) { /* Handling of Q_tot coming from bio_rho.cgi. Json does not work right now, probably problem on

Re: [Jmol-users] renaming Object Jmol files

Good idea ! Shall we bundle them in a single mimized js file ? Paul Le 12 juin 2012 à 20:49, Robert Hanson a écrit : I think I need to rename these so that they appear together and also are easy to copy from one place to another: JmolCore.js -- Jmol_Core.js JmolApplet.js--

Re: [Jmol-users] renaming Object Jmol files

Evans evan...@illinois.edu wrote: A good idea from the standpoint of loading speed. Cheers, Mike --- Mike Evans Organic Chemistry Graduate Student, Moore Group University of Illinois, Urbana-Champaign On Thu, Jun 14, 2012 at 4:30 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr

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

Might be relevant to this discussion, I'm setting up a script to replace a Jmol png image (with state included) by an applet when user hovers the image and click on a link then displayed. The first attempt can be seen there : http://librairiedemolecules.education.fr/molecule.php?idmol=336 Try

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

Thanks Angel ! (I don't know why messages didn't go to the list yesterday) I've tried it at my school today with their IE8 and discovered exactly the same behavior as you described. But I've tried it with other images such as the ones on this page

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

Le 11 juin 2012 à 21:10, Angel Herráez a écrit : Testing in IE9 (64-bit, Win7): The IE console reports a javascript error at line 31, jmol = Jmol.getApplet( jmol, Info) that's because is should be : jmol = Jmol.getApplet( jmol, Info) (without quotes)

Re: [Jmol-users] Eval Function

Have you tried this approach : script APPLET appletName @{Jmol math expression} (from the documentation) Paul Le 17 mai 2012 à 18:46, Otis Rothenberger a écrit : Bob, Is there a way to execute JmolScript that is in a string variable - i.e. an eval function approach? Otis -- Otis

Re: [Jmol-users] Eval Function

Too quick ! The following is even better for your purpose : script INLINE @{Jmol math expression} Runs the script command result of the Jmol math expression rather than from a file. The math expression may be a simple single variable name or a more complex expression. For example, var

Re: [Jmol-users] Jmol partial charge calculation

Otis, I think the green surface is great and I was just wondering how it could be displayed for alkanes. My guess is that it's not displayed because when there is no partial charge, no MEP surface can be created. The problem is how does Jmol guess there is no partial charge in the file?, and

Re: [Jmol-users] Jmol partial charge calculation

I am not an expert here... Is there a significative change in computational time or in the results obtained from what can be done with the currently implemented UFF ? Paul Le 9 mai 2012 à 02:50, Robert Hanson a écrit : I guess the next step is to implement MMFF94 in Jmol. I had been avoiding

Re: [Jmol-users] Jmol partial charge calculation

This is brilliant ! In case somebody is wondering how to display labels showing the partial charges : label %[partialCharge] Paul Le 8 mai 2012 à 22:04, Robert Hanson a écrit : OK, this is working. http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm load a model by name from

Re: [Jmol-users] Jmol/ChemDoodle -- test2

How does this work technically (JSONP ? other ?) ? I thought it was not possible to make ajax calls to other domains without triggering a security message (to prevent cross site scripting) ? It's very exciting to see this working so well without the signed applet ! Paul Le 21 avr. 2012 à 01:56,

Re: [Jmol-users] Jmol/ChemDoodle -- test2

Bob, I am still working on a rewrite of Jmol.js It takes time, but my efforts are going in the same way as the library you made. Hope I could make it available soon. Paul Le 17 avr. 2012 à 14:11, Robert Hanson a écrit : 2012/4/17 Angel Herráez angel.herr...@uah.es Specifically,

Re: [Jmol-users] Jmol/ChemDoodle -- test1

How does this work ? It apparently makes a call to a php script hosted on stolaf's server. Does this php script itself calls jmoldata.jar server side ? And how does it replies ? by sending back a mol file or a chemdoodle JSON object ? -Paul

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