[Jmol-users] JSmol-related book about molecular modeling in chemistry education

*Dear Jmol users* Me and my two colleagues, we wrote a small introductional book for molecular modeling in chemistry education. It is a chemistry educational application of JSmol. The book includes theoretical background suitable for chemistry teachers, chemistry educational researchers and

Re: [Jmol-users] JSmol labels on zoom

Hi Jaime It's always been like that by default, but I think there is an option: set fontscaling on although it is a little tricky to get it working when there is zoom between two applications of labels. See https://chemapps.stolaf.edu/jmol/docs/?ver=14.6#font

[Jmol-users] JSmol labels on zoom

There’s not a proportional change of size of Labels when zooming a model on JSmol 14.9.1 (and maybe on other versions), both on zooming initiated by script and by interactive mouse driven. Labels remain with the original font size despite the change in size of the model. Is there a way to

Re: [Jmol-users] JSmol applet creation of mo surfaces or contour plot is slow

Hello Bruce I will gladly take a look at your page when I have time, but here are a few comments in advance: 1. Using JSmol-html5 with IE is very slow, indeed. Other browsers are recommendable. 2. Given the current state of Java support, you'd better forget chances of using Jmol-Java. I

[Jmol-users] JSmol applet creation of mo surfaces or contour plot is slow

Over the last couple of years I have created a number of web pages using Jmol, to support research publications in inorganic main-groups chemistry or for undergraduate teaching. I have created a portfolio web page https://www.staff.ncl.ac.uk/bruce.tattershall/jmolapps/portfolio.html showing

Re: [Jmol-users] Jsmol mutate behaviour

Angel suggested yesterday the minimizing solution which works. Thank you both! Jaim Here’s Angel complete solution: mutate 148 SER; select [SER]148:A; color CPK; wireframe 0.2; color opaque; minimize (selected and sidechain); // alternative: minimize fix (not (selected and sidechain));

Re: [Jmol-users] Jsmol mutate behaviour

(sorry for the delay -- the images were over the byte limit for the list) I just meant that I think the flexible fit algorithm in Jmol just uses the carbon atoms, not the rest of the atoms, so it is quite possible that a C-O bond will be rotated. Did you try minimizing? ​

Re: [Jmol-users] Jsmol mutate behaviour

On 29 Jan 2017, at 2:39 PM, Robert Hanson > wrote: Might be just the carbon atoms. Can you please be more explicit? What I’m doing wrong? Is there a way to apply the mutate command and get the correct rendering?

Re: [Jmol-users] Jsmol mutate behaviour

Might be just the carbon atoms. On Sun, Jan 29, 2017 at 3:31 AM, Jaime Prilusky < jaime.prilu...@weizmann.ac.il> wrote: > > Something funny on the results I get from the mutate command. > > By mutating a residue into the same residue, I was expecting no > conformational change. > > What I’m

[Jmol-users] Jsmol mutate behaviour

Something funny on the results I get from the mutate command. By mutating a residue into the same residue, I was expecting no conformational change. What I’m doing wrong? Same results with jsmol_14.6.1_2016.08.11 and jsmol_14.7.5_2016.12.02 Please see the attached image. The same structure

Re: [Jmol-users] JSmol submenus not working in iOS

://www.chemtube3d.com > Tel: +44 (0)151-794-3506 (3526 Student Support Office) > > > On 22 Oct 2016, at 01:54, jmol-users-requ...@lists.sourceforge.net wrote: > > Date: Thu, 20 Oct 2016 12:05:07 -0500 > From: Otis Rothenberger <osrot...@icloud.com> > Su

Re: [Jmol-users] JSmol submenus not working in iOS

:54, jmol-users-requ...@lists.sourceforge.net<mailto:jmol-users-requ...@lists.sourceforge.net> wrote: Date: Thu, 20 Oct 2016 12:05:07 -0500 From: Otis Rothenberger <osrot...@icloud.com<mailto:osrot...@icloud.com>> Subject: Re: [Jmol-users] JSmol submenus not working in

Re: [Jmol-users] JSmol submenus not working in iOS

Nick, I “buttonize" everything I need in my app, so I never brought the iPad Jmol menu issue up, but I agree. It would be nice if it worked in an iPad. Bob, you were probably joking, but I have a iPad up for grabs! The problem I have is it’s in Florida, and I’m in Normal IL for an ISU

Re: [Jmol-users] JSmol submenus not working in iOS

> The text field would be a solution but a functional menu would be better. The menu is managed by jQuery-UI so the fix should come from there. I guess there is some mobile-friendly jQuery Jmol users Maybe we should raise funds to buy Bob that iPad ! crowdfunding is the fancy word now ;-)

Re: [Jmol-users] JSmol submenus not working in iOS

If someone gives me an iPad, I can see if I can fix that :) Bob On Thu, Oct 20, 2016 at 10:00 AM, Philip Bays wrote: > My observation (iPad) is that it opens but none of the links work and you > close it by trying to drag it. > > > On Oct 20, 2016, at 10:39 AM, Otis

Re: [Jmol-users] JSmol submenus not working in iOS

.@icloud.com>> Subject: Re: [Jmol-users] JSmol submenus not working in iOS To: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net> Message-ID: <19198363-1e17-492b-9581-74c3f3dfb...@icloud.com<mailto:19198363-1e17-492b-9581-74c3f3dfb...@icloud.com>> Content-Typ

Re: [Jmol-users] JSmol submenus not working in iOS

My observation (iPad) is that it opens but none of the links work and you close it by trying to drag it. > On Oct 20, 2016, at 10:39 AM, Otis Rothenberger wrote: > > Nick and Bob, > > I keep my eyes on iPad/Jmol performance pretty closely. I don’t think this > ever

Re: [Jmol-users] JSmol submenus not working in iOS

Nick and Bob, I keep my eyes on iPad/Jmol performance pretty closely. I don’t think this ever worked. You can’t even touch-close the console if you open it with the console command. I just assumed this was an iPad thing. That’s why I include my own text field for Jmol Script. JQuery does have

Re: [Jmol-users] JSmol submenus not working in iOS

I tried Safari and Firefox on a desktop and found no problem. Is it the touch interface? On Thu, Oct 13, 2016 at 1:47 PM, Greeves, Nick wrote: > I’ve tested an iPhone and an iPad running iOS 10. > > Load a page running JSmol, click on the logo, choose any of the items

[Jmol-users] JSmol submenus not working in iOS

I’ve tested an iPhone and an iPad running iOS 10. Load a page running JSmol, click on the logo, choose any of the items with a submenu e.g. Console or Surfaces, nothing happens for me. I’m pretty certain this used to work. Anyone else? Best regards Nick -- Nick Greeves

Re: [Jmol-users] JSMOL load inline function

Glad you solved it As far as I remember, the pipe character serves the same as your \n Inline loading is always tricky! On 26 Sep 2016 at 12:49, Matthew Kennedy wrote: Thank you Angel, in the end, it appears the issue was that it needs to print out the literal \n's in the script line. So

Re: [Jmol-users] JSMOL load inline function

Thank you Angel, in the end, it appears the issue was that it needs to print out the literal \n's in the script line. So the following worked for me: script: 'load inline "25\n 0QURM735R7BTNZJNL\n C 1.417382 -0.002747 -0.016830 \n C -0.728040 1.261000 0.12 \n C -0.728040 -1.261000 0.12

Re: [Jmol-users] JSMOL load inline function

You may also need a space between the pipe and the element symbol, so it seems > that lacks newline characters apparently. Jmol needs either those or > vertical > lines (the 'pipe' character, | ) Try inserting a pipe before each new line·

Re: [Jmol-users] JSMOL load inline function

Mathew, that lacks newline characters apparently. Jmol needs either those or vertical lines (the 'pipe' character, | ) Try inserting a pipe before each new line· Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares

Re: [Jmol-users] JSMOL load inline function

Hi Angel, The script line is as follows: script: 'load inline "25 0QURM735R7BTNZJNL C 1.417382 -0.002747 -0.016830 C -0.728040 1.261000 0.12 C -0.728040 -1.261000 0.12 C -0.000200 -0.001120 -2.476610 C 0.681964 -1.257343 -2.046422 C 0.689513 -1.259021 -0.497124 C 0.686920

Re: [Jmol-users] JSMOL load inline function

Hi Mathew Possible sources of trouble (just a guess) - quotes (particularly when they get nested) - line breaks all that related to Javascript handling of your text string If you could provide a sample as plain text of what the php variable outputs., it would help diagnosis. Another idea:

[Jmol-users] JSMOL load inline function

Dear all, I have the following code inside a jsmol applet embedded in an html page with some php at the top. script: 'load inline ;' This code correctly prints out the expected geometry but when it is loaded into the jsmol applet on the page, it is completely incorrect compared to if I load

Re: [Jmol-users] JSmol in Institutional Repositories?

Hi Vin Can you explain more what you are after? I know Dspace only as something related to libraries, either a way to store references or full articles (not sure now) JSmol files are stored in any server that is holding webpages with models. What kind of application or use are you thinking of?

[Jmol-users] JSmol in Institutional Repositories?

Hello, I have seen many great incorporations of JSmol in chemical databases and web pages. However, I am curious if anyone has incorporated JSmol into an Institutional Repository (e.g. Dspace)? Thanks! Vin Vincent F. Scalfani, Ph.D. Science and Engineering Librarian, University Libraries

Re: [Jmol-users] Jsmol in GWT

My guess is that GWT is not designed to interact with external pieces. Could that be? You should do everything with the uncompressed files: cd jsmol copy js/JSmol.full.js JSmol.min.js copy j2s/core/corejmol.js j2s/core/corejmol.z.js But yes, that sounds like you have the issue there. Try

Re: [Jmol-users] Jsmol in GWT

In function Displays.drawImage the buf8 field is undefined. The reason is probably calling imageBuffer = this.getImage (false, false); in Viewer.js:2207. In working code it returns but in my code it's only: And in html code is still: myJmol._cover(false) Any ideas? On 2016-08-01 15:53:07,

Re: [Jmol-users] Jsmol in GWT

Thanks Robert, adding window.myJmol = myJmol helped, but there is another problem. This is log from browser console: JSmol load myJmol loadClazz... JSmol load myJmol start applet... JSmol exec myJmol loadClazz null -- OK xhr.open async=false url=jsmol/j2s/core/package.js Synchronous

Re: [Jmol-users] Jsmol in GWT

You could add an alert to see if myJmol has been created: var applet = Jmol.getAppletHtml("myJmol", Info); alert(self.myJmol) ​Or, it is possible that somehow the myJmol variable is not being set globally, in which case you could try: var applet = Jmol.getAppletHtml("myJmol", Info);

Re: [Jmol-users] Jsmol in GWT

Hi Tom All looks good, but I am not familiar with the GWT environment. There might be some confilct. One question: When are you calling that code? Is the "myContainer" node already created? The error is not helpful, but you could try defining the variable at the beginning (head section) as

[Jmol-users] Jsmol in GWT

Hello, Using Jsmol 14.6.1, I can not load applet inside GWT application using native js. Bellow my code: var Info = {     height: "90%",     width: "90%",     color: "#00",     j2sPath: "jsmol/j2s",     use: "HTML5",     script: "load ${fileUrl}",     disableJ2SLoadMonitor: true,    

Re: [Jmol-users] JSmol

Sounds about right. You cannot tell that you are not using Java, except for the performance. The Java language is being implemented *as* JavaScript. x = new java.util.Hashtable() Object { elementCount: 0, elementData: Array[11], loadFactor: 0.75, threshold: 8, firstSlot: 11, lastSlot: -1,

[Jmol-users] JSmol

Bob, Maybe everyone got this from the beginning, but it’s kind of an epiphany to me if I’m now correct in my understanding: Jmol to JSmol was not a translation of Java to Javascript. Rather the process brought Jmol (Java) under a JavaScript blanket. If we are woking outside this blanket, we

Re: [Jmol-users] JSmol inside tables?

Hi John It is the same way. You can put the Jmol.getApplet() call inside each table cell. http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Functions#getApplet You will need to use/define 4 different variables for the 4 JSmol objects. A single Info variable may be shared by all.

[Jmol-users] JSmol inside tables?

Hi All, With the Jmol applet,placing a jmolApplet script between tags displays the molecule in that cell of the table on the webpage. For example, with four cells in a table, I can display 4 different molecules. How can I do this with JSmol.min.js ? What goes between the tags? John Keller

Re: [Jmol-users] jsmol does not activate molecule automaticaly (moodle)

Le 06/03/2016 18:23, Robert Hanson a écrit : > See https://docs.moodle.org/30/en/Jmol_filter where it indicates that you > need > to add a search item ?i=0 to your URL: Nice... it's work ! I use moodle 2.9 and read the 2.9 documentation where "?i=0" is not documented but it's work with this

Re: [Jmol-users] jsmol does not activate molecule automaticaly (moodle)

See https://docs.moodle.org/30/en/Jmol_filter where it indicates that you need to add a search item ?i=0 to your URL: *?i=0* results in the interactive structure being displayed directly (i.e. with no cover image). This may result in page load delays if, say, multiple Jmol objects are present in

Re: [Jmol-users] jsmol does not activate molecule automaticaly (moodle)

Hello Christian That is a feature of JSmol that may or not be enabled. It may involve one of these options: - coverImage - deferApplet - deferUncover (most probably the 2nd) They are described in http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Startup_period It seems that the

[Jmol-users] jsmol does not activate molecule automaticaly (moodle)

Hello, I use jmol filter in moodle and I have a problem with it. When I include a molecule in my moodle, the applet work fine, but I need to click on the applet. (button with circular arrow and "activat 3D model" hint) (view screenshot) How can I activate automaticaly the model, without

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

nice. Yes, saving the state would be more general: Jmol.getPropertyAsString("stateInfo") Otis, what events exactly are you using for triggering the save and restore scripts? > var stash = localStorage.getItem("chemagicTEMP”); > if (stash == null || stash == undefined || stash == "") { stash =

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

Bob, I do it with explicit links that leave the page, but it should work with onbeforeunload to automate it. The return is taken care of in the app (model kit). The return to model kit is handled in the Jmol ready callback. If the special memory location is not null, then the memory data is

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

On 02/12/2016 02:33 AM, Otis Rothenberger wrote: > It turns out that there is a JQuery solution to the Safari back/forward > browser cache issue: > > $(window).bind("pageshow", function(event) { > if (event.originalEvent.persisted) { > window.location.reload() > } > }); > >

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

Hmm. I don't know if I like that as a default. People don't like surprises, and I really dislike it personally when a page disables the "back" function. ​ Bob -- Site24x7 APM Insight: Get Deep Visibility into Application

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

Am 12.02.16 um 20:29 schrieb Robert Hanson: > Hmm. I don't know if I like that as a default. People don't like > surprises, and I really dislike it personally when a page disables the > "back" function. > ​ I wasn't suggesting this as a general default. With a complex tool like the 'Jena3D

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

On Fri, Feb 12, 2016 at 1:52 PM, Rolf Huehne wrote: > > And the "back" function actually isn't totally disabled. At least in > Firefox and Safari (not tested in other browsers) the "click and hold" > function to select a specific step in the history still works. > >

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

For what it’s worth, here is the code to use browser local storage to “stash” a model when you leave a JSmol page. I’m using the molfile, but Jmol state/restore should also work - See note at end of email. An extension of the approach should also allow you to save/reset JavaScript variables

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

I’ve noticed this for quite some time with the browser back button. I think it’s a browser page cache issue. The browser is not communicating with the server after a back button click. Maybe Bob can do something to defeat this in JSmol, but I think you need control of your server’s http headers

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

On 02/11/2016 07:41 PM, Jaime Prilusky wrote: > It seems that JSmol gets unloaded when a page gets out of focus, by flipping > between pages, on Safari Mac Version 9.0.3 (11601.4.4). > > 1. Open any page on Safari Mac (tested on Version 9.0.3) > > 2. Now open a page with JSMol on it, i.e.

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

Very Interesting! On Mac, FF and Chrome reload the JSmol page on back button. I mean fresh reload! You get a default model reload. I was missing this because of my local storage approach. The back button was reloading the page with FF and Chrome, but the reload was loading my last model via

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

I confirm this behavior. You can go back and forth if they are loaded in tabs or different pages, but not via history. Same Safari version. In Firefox and Chrome, the applet reloads on return. > On Feb 11, 2016, at 1:41 PM, Jaime Prilusky > wrote: > > It

Re: [Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

It turns out that there is a JQuery solution to the Safari back/forward browser cache issue: $(window).bind("pageshow", function(event) { if (event.originalEvent.persisted) { window.location.reload() } });

[Jmol-users] JSmol on Safari Mac Version 9.0.3 (11601.4.4)

It seems that JSmol gets unloaded when a page gets out of focus, by flipping between pages, on Safari Mac Version 9.0.3 (11601.4.4). 1. Open any page on Safari Mac (tested on Version 9.0.3) 2. Now open a page with JSMol on it, i.e. http://proteopedia.org/w/1dnn 3. Go to the previous page:

Re: [Jmol-users] JSmol defaults for label ?

I was hoping to find a single statement or two that would cause the fault. Somehow I did not stumble on that. But I also see some other issues so will get onto those as well. >From Jamaica, Bob On Sun, Jan 3, 2016 at 10:18 AM, Jaime Prilusky < jaime.prilu...@weizmann.ac.il> wrote: > See

Re: [Jmol-users] JSmol defaults for label ?

Can you please implement defaults again? Jaim On 3 Jan 2016, at 3:33 PM, Robert Hanson > wrote: Yes, that's something I changed. Darn. When does it happen? On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky

Re: [Jmol-users] JSmol defaults for label ?

Please give me a script I can test. On Sun, Jan 3, 2016 at 9:57 AM, Jaime Prilusky < jaime.prilu...@weizmann.ac.il> wrote: > Can you please implement defaults again? > > Jaim > > On 3 Jan 2016, at 3:33 PM, Robert Hanson wrote: > > Yes, that's something I changed. Darn. When

Re: [Jmol-users] JSmol defaults for label ?

See http://proteopedia.org/wiki/tests/tstscene.html Click on [scene 2] to load the scene. The same scene works Ok after setting some font and alignment attributes (find "enabling the following defaults” in the script) On 3 Jan 2016, at 4:58 PM, Robert Hanson

Re: [Jmol-users] JSmol defaults for label ?

Yes, that's something I changed. Darn. When does it happen? On Sun, Jan 3, 2016 at 6:18 AM, Jaime Prilusky < jaime.prilu...@weizmann.ac.il> wrote: > Unless we set defaults for labels, we get the following JSmol error: > this.colixes is null, when using Jmol 14.4.1 2015-12-23 > > Same script

Re: [Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

Hooray! And that will not be necessary in the next release On Thu, Dec 17, 2015 at 6:26 AM, Rolf Huehne wrote: > On 12/17/2015 12:27 AM, Robert Hanson wrote: > > Please do give that a try and report back if the "syntax error" message > > disappear. I had never made the

Re: [Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

On 12/17/2015 12:27 AM, Robert Hanson wrote: > Please do give that a try and report back if the "syntax error" message > disappear. I had never made the connection that those were only when > loading local files. > The syntax error messages I reported are all gone in Firefox on MacOS X Mavericks

[Jmol-users] JSmol speed vs. browsers

I have provided data, methods and detailed conclusions here *http://proteopedia.org/w/JSmol/Rotation_Speeds* Briefly I found: For JSmol (HTML5/javascript) Firefox outperforms Chrome, Opera and Edge by about four-fold. Safari is as fast as Firefox with JSmol. Internet Explorer 11 is unusably

[Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

Hi all, with JSmol/HTML5 I get a lot of Javascript error messages in Firefox 42 on Linux if I load the page locally from the file system. The error messages don't occur in Chromium 31 or if the page is loaded from a web server. Although JSmol still seems to work properly it seems especially

Re: [Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

Ho, ho. What luck. A little web digging turned up the solution. Add this to your page: $.ajaxSetup({ mimeType: "text/plain" }); I will get that into JSmol. Bob On Wed, Dec 16, 2015 at 11:46 AM, Rolf Huehne wrote: > Hi all, > > with JSmol/HTML5 I get a lot of

Re: [Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

Please do give that a try and report back if the "syntax error" message disappear. I had never made the connection that those were only when loading local files. On Wed, Dec 16, 2015 at 4:43 PM, Eric Martz wrote: > Rolf, Bob and everyone, I, too, have noticed these

Re: [Jmol-users] JSmol 14.4.1 - Javascript error messages in Firefox 42

Rolf, Bob and everyone, I, too, have noticed these numerous error messages in Firefox when running from local files in OS X. Since everything seemed to work, I didn't worry about them much. But it would be nice to eliminate them so it would be easier to find the errors that matter. Thanks,

[Jmol-users] JSmol in Edge, Chrome, etc.

My tests of JSmol (in FirstGlance) in the Windows 10 Edge browser indicate that while Edge runs HTML5/Javascript much faster than Internet Explorer, it is still markedly slower than Chrome or Firefox. Internet Explorer remains unusably slow with JSmol/HTML5. Edge is usable but sluggish,

Re: [Jmol-users] JSmol in Edge, Chrome, etc.

Thanks for the summary, Eric. Quite the moving target. ​ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] JSmol loading of binary files?

Hi folks Just noticed that JSmol (14.2.15_2015_07_09) appears to be loading binary files (.pse, .pdb.gz, .png) using Chrome (45.0.2454.101), Chromium ( 45.0.2454.99) or Edge without using jsmol.php. e.g. I can comment out serverURL: from var Info, without any obvious issues. Has there been a

Re: [Jmol-users] JSmol loading of binary files?

No recent changes in JSmol. On Mon, Oct 12, 2015 at 5:49 AM, Geoffrey Rowland wrote: > Hi folks > > Just noticed that JSmol (14.2.15_2015_07_09) appears to be loading binary > files (.pse, .pdb.gz, .png) using Chrome (45.0.2454.101), Chromium ( > 45.0.2454.99) or Edge

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

​This can happen if something on the page tells Jmol that HTML5 is not allowed, which is supposed to be only the case for MSIE 8. JSmolApplet.js: case "HTML5": if (Jmol.featureDetection.allowHTML5){ applet = Applet._getCanvas(id, Info, checkOnly, false); }

Re: [Jmol-users] JSmol: how to change an atom's B-factor?

[Jmol-users] JSmol: how to change an atom's B-factor? Am 30.09.15 um 22:51 schrieb Luciano Abriata: > Thanks Angel. There is one thing I cannot yet solve, what if I refer to > my atom of interest as residuenumber:chain.atom ? > > For example, > > 37:a.ca > > works a

[Jmol-users] JSmol/HTML5 - Forced usage

Hi all, is there a way to force JSmol to use HTML5 and not Java instead of just providing a priority list? My problem is that JSmol 14.3.16_2015.09.28 on a specific page always runs the Java version even though the priority is set to "HTML5" and "JAVA" isn't even included in the priority

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] JSmol/HTML5 - Forced usage

Rolf, there is no reason it would use Java if it is not declared in the Info variable. Check that you are indeed defining Info.use = 'html5' and it is not being overwritten somewhere else The url parameter will probably force the modality, as Paul indicated, but still you must find the

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

On 10/01/2015 04:55 PM, Paul PILLOT wrote: > 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 > Thanks, Paul. Because it is a static page I had tried

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

On 10/01/2015 06:33 PM, Angel Herráez wrote: > > Rolf, there is no reason it would use Java if it is not declared in the Info > variable. > > Check that you are indeed defining Info.use = 'html5' and it is not being > overwritten somewhere else > The 'Info' variable is declared like this:

[Jmol-users] JSmol: how to change an atom's B-factor?

Dear all, How can I change the B-factor of an atom in a loaded PDB, by another number coming from calculations inside my program? (I want this so as to color-code data on the structure using color RELATIVETEMPERATURE) Thanks in advance for your help, Luciano

Re: [Jmol-users] JSmol: how to change an atom's B-factor?

Am 30.09.15 um 21:14 schrieb Luciano Abriata: > Dear all, > > How can I change the B-factor of an atom in a loaded PDB, by another > number coming from calculations inside my program? > > (I want this so as to color-code data on the structure using color > RELATIVETEMPERATURE) > The B-factor is

Re: [Jmol-users] JSmol: how to change an atom's B-factor?

Hi Luciano Please see the list of atom properties: http://chemapps.stolaf.edu/jmol/docs/#atomproperties What you want is "temperature", like this: load =1crn; color temperature; {atomNo=24}.temperature = 30; color temperature; Another choice is to use a custom property and then apply color

Re: [Jmol-users] JSmol: how to change an atom's B-factor?

Am 30.09.15 um 22:51 schrieb Luciano Abriata: > Thanks Angel. There is one thing I cannot yet solve, what if I refer to > my atom of interest as residuenumber:chain.atom ? > > For example, > > 37:a.ca > > works as a selection command (atom CA in chain A in residue 3), but > instead this or similar

Re: [Jmol-users] JSmol: how to change an atom's B-factor?

to work. Any clue? Thanks again Luciano De: Angel Herráez <angel.herr...@uah.es> Para: Luciano Abriata <luciano_abri...@yahoo.com>; jmol-users@lists.sourceforge.net Enviado: Miércoles, 30 de septiembre, 2015 21:43:28 Asunto: Re: [Jmol-users] JSmol: how to change an atom's B-fa

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

for the record, this is fixed. On Tue, Sep 15, 2015 at 1:08 PM, Robert Hanson wrote: > Sorry, dropped off the TODO list. It's back on. > > On Tue, Sep 15, 2015 at 2:02 AM, Johannes | Edumol > wrote: > >> Any news on this? >> Can this be fixed? >> >> And

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

Any news on this? Can this be fixed? And why only some molecules are downloaded again, but e.g. but if molecule includes only carbon and hydrogen atoms it can be switched side side without new downloading. On 19.8.2015 1:23, Robert Hanson wrote: ​Very interesting. Thanks! How did you do

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

Sorry, dropped off the TODO list. It's back on. On Tue, Sep 15, 2015 at 2:02 AM, Johannes | Edumol wrote: > Any news on this? > Can this be fixed? > > And why only some molecules are downloaded again, but e.g. but if molecule > includes only carbon and hydrogen atoms it can be

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

I think it died years ago. On Thu, Aug 27, 2015 at 2:57 PM, Stephen Hillier stephen.hill...@hutton.ac.uk wrote: Can anyone advise if JSmol will run via the liveweb addin in Powerpoint? I've located some similar questions like this before in the archive but was unable to locate an answer

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

Steve, Flip it! Turn the logic around. For PPT and Keynote, batch converting a slide presentation into images is fast and simple. With the images in hand make an html image slide show template that uses an unordered list (ul) with each li a slide image. There are a number of templates on the

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

On 28 Aug 2015, at 19:11, Otis Rothenberger osrot...@chemagic.com 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

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

I received an off list question that I’ll answer on list because it might be of general interest: Could you play a ppt animation by this method? Sure, this is HTML5! Those li/li holders can hold almost any legal html. I have not tried it, but I’m almost certain they even could hold a JSmol

[Jmol-users] JSmol via liveweb in Powerpoint?

Can anyone advise if JSmol will run via the liveweb addin in Powerpoint? I've located some similar questions like this before in the archive but was unable to locate an answer describing how to do it. I have a page that will run locally in a browser without issue. However, when I point to

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

I uploaded the video to GoogleDrive, set the file public and then it can be shared via link. Very handy to sent small screencasts / -captures. Any cloud storage service can provide this link share option. On 19.8.2015 1:23, Robert Hanson wrote: ​Very interesting. Thanks! How did you do that

[Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

Hi all. There seems to be a bug in JSmol-JSME-integration: 1) For some molecules, like aspirine, the JSmol side downloads the molecule from database again every time when switching from back from the 2D-side. Even if there is no modifications made to the structure in the 2D-side. Test:

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

How can you do that on html please give me demo Amitesh kumar sharma Noida Uttar Pradesh On Tue, Aug 18, 2015 at 3:16 PM, Johannes | Edumol edu...@edumol.fi wrote: Hi all. There seems to be a bug in JSmol-JSME-integration: 1) For some molecules, like aspirine, the JSmol side downloads the

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

​Very interesting. Thanks! How did you do that link, by the way? (I thought we couldn't do attachments, so I'm guessing that is just a link to a file, not the file itself. But I don't know how to do that.) --

Re: [Jmol-users] JSmol-JSME integration bug: 3D-side is downloading the molecule again when switching back from 2D

demo about to integrate with html Amitesh kumar sharma Noida Uttar Pradesh On Wed, Aug 19, 2015 at 3:53 AM, Robert Hanson hans...@stolaf.edu wrote: ​Very interesting. Thanks! How did you do that link, by the way? (I thought we couldn't do attachments, so I'm guessing that is just a link to

Re: [Jmol-users] JSMol Sync function

yes. See http://chemapps.stolaf.edu/jmol/jsmol/sync4.htm On Mon, Aug 10, 2015 at 11:40 AM, Thomas Hrabe thr...@gmail.com wrote: Hi everyone, I was trying to get the sync function running with the recent JSMol API, but no success. Is that functionality still supported in the more recent

[Jmol-users] JSMol Sync function

Hi everyone, I was trying to get the sync function running with the recent JSMol API, but no success. Is that functionality still supported in the more recent JSMol APIs? Thanks, Thomas --

Re: [Jmol-users] JSMol sync views

See http://chemapps.stolaf.edu/jmol/jsmol/sync4.htm Right, the applets do not share memory. It illustrates how to do applet synchronization. The basic idea is that that the SYNC command allows you to send commands around to one or more specific applets from a master applet. Then you can just

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