Re: [Jmol-users] JSmol popup menu when in iframe?

On 11/10/2014 02:36 PM, Geoffrey Rowland wrote: > Hi folks > > In some situations, it can be really useful to embed a JSmol instance in an > inline frame. Particularly when using JSmol with, say, CMS systems that use > JavaScript libraries that conflict with JSmol. Note that this use-case does > no

[Jmol-users] JSmol popup menu when in iframe?

Hi folks In some situations, it can be really useful to embed a JSmol instance in an inline frame. Particularly when using JSmol with, say, CMS systems that use JavaScript libraries that conflict with JSmol. Note that this use-case does not involve cross-domain issues. Just using an iframe to 'ins

Re: [Jmol-users] JSMol : Problem loading second structure after button click

Hi Thomas There may be no need for any changes in the other server; please try my code at the bottom. You MUST define the location of jsmol.php That cod works for me in localhost, but nt when I upload to my server. That may be related to Bob's comments about AJAX calls, I don't know about that.

Re: [Jmol-users] JSMol : Problem loading second structure after button click

My guess is that the page doing this (maybe local to your computer?) is not within the http://cancer3d.org domain. In that case, Jmol cannot assume that that domain allows AJAX loading across domains. But it it more interesting than that. The file

Re: [Jmol-users] JSMol : Problem loading second structure after button click

Hi Thomas What that message says is that to load the 2nd file (probably because it comes from a different server) the use of the jsmol.php component is needed, and you have not properly configured the location of that file. ("your.server.here" is a placeholder for the actual location, that you m

[Jmol-users] JSMol : Problem loading second structure after button click

Hi all, I want to display a new structure in a JSMol window where another structure is being displayed. I keep getting this error alert message: Error connecting to server: http://your.server.here/jsmol.php?call=getRawDataFromDatabase&database=_&query=http%3A%2F%2Fcancer3d.org%2FstructuresChain

[Jmol-users] JSmol site

Check it out! http://sbkb.org/fs/trkh-potassium-ion-transporter -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take wh

Re: [Jmol-users] JSmol crash (Jmol applet OK)

That problem relates to using .sort() and .count() and perhaps a few more math functions. Possibly also GIF file creation. On Sat, Sep 20, 2014 at 4:08 PM, Robert Hanson wrote: > casualty of recent work optimizing efficiencies > > http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.20b.zip >

Re: [Jmol-users] JSmol crash (Jmol applet OK)

casualty of recent work optimizing efficiencies http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.20b.zip On Sat, Sep 20, 2014 at 2:12 PM, Eric Martz wrote: > An expression that I use in FirstGlance to count the number of each kind > of ligand or non-standard residue is crashing recent ve

[Jmol-users] JSmol crash (Jmol applet OK)

An expression that I use in FirstGlance to count the number of each kind of ligand or non-standard residue is crashing recent versions of JSmol, but not Jmol/Java. An example of the expression: {[TRS] and hetero}.groupindex.all.count().length (I was unable to guess how to make such a count, and

Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

0)7909 586624 Fax: +44(0)1235 567801 Skype: chris_c_wood From: Mark Wass [m.n.w...@kent.ac.uk] Sent: 03 September 2014 10:33 To: jmol-users@lists.sourceforge.net Cc: Mark Wass Subject: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary Hi,

Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

Did you try that link? I see Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at y...@example.com to inform them of the time this error occurred, and the actions you performed just

Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

On Sep 3, 2014, at 12:49 PM, Mark Wass mailto:m.n.w...@kent.ac.uk>> wrote: Thanks for the suggestion Jaim. It works properly in firefox but not in Safari. Is there a fix to get it working in Chrome and Safari? I’m also looking for a solution :-) I remember for this or a related problem being me

Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

ourceforge.net>" mailto:jmol-users@lists.sourceforge.net>> Date: Wednesday, 3 September 2014 10:41 To: "jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>" mailto:jmol-users@lists.sourceforge.net>> Subject: Re: [Jmol-users] JSmol - Unab

Re: [Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

This seems to be a Chrome problem. Try with Firefox or Safari before trying to fix your server. Jaim On Sep 3, 2014, at 12:33 PM, Mark Wass mailto:m.n.w...@kent.ac.uk>> wrote: Hi, I am currently trying to get Jsmol to work on my server. I have used Jsmol successfully on other servers but this

[Jmol-users] JSmol - Unable to load PDB file appears to think it is binary

Hi, I am currently trying to get Jsmol to work on my server. I have used Jsmol successfully on other servers but this time I can’t get it to work. As a test I am simply trying to load a PDB file but when I try to load the page I get the following message: Error connecting to server: http://ww

Re: [Jmol-users] JSMol select residue by mouse callback

Hi Thomas You need to set a callback function Please see http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Callbacks http://chemapps.stolaf.edu/jmol/docs/#setcallback or maybe http://chemapps.stolaf.edu/jmol/docs/#getproperty -

[Jmol-users] JSMol select residue by mouse callback

Hi everyone, how can I specify a function to capture mouse clicks into the structure / on a residue. What I aim at is to read the residue ID and display some additional information about it. Thanks, Thomas -- Want fast

Re: [Jmol-users] JSmol write protected Console?

Background is that I found that jQuery is not reporting consistent information for keyboard events across browsers, and I went in and changed the way how Jmol is responding to those events in JavaScript. This is just the sort of problem I expect. I will get a new version out today, and then if you

Re: [Jmol-users] JSmol write protected Console?

I have to look at the code for Console, which is broken at this moment on my local version. -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of B

Re: [Jmol-users] JSmol write protected Console?

I am currently using jmol-14.2.2_2014.06.29 on Chrome, and while I can write most characters into the console, I cannot type the character "(", which is used in a lot of script commands. I've had this trouble before in much older versions of JSmol (I think around June of last year), so I was wonde

Re: [Jmol-users] JSmol PHP file

On Tue, Jul 15, 2014 at 4:30 AM, wrote: > As a follow up to the recent discussion about Firefox 30, and the use of > the PHP file, there are a few issues I’d like to get sorted in my head; my > current understanding / questions: > > > > - If JSmol is being hosted on a remote server (i.e

[Jmol-users] JSmol PHP file

As a follow up to the recent discussion about Firefox 30, and the use of the PHP file, there are a few issues I'd like to get sorted in my head; my current understanding / questions: - If JSmol is being hosted on a remote server (i.e. a website), and the developer has an option to all

Re: [Jmol-users] JSmol write protected Console?

Found it. Will upload new version soon. On Wed, Jun 18, 2014 at 5:32 AM, Jaime Prilusky < jaime.prilu...@weizmann.ac.il> wrote: > >From my server with Jmol 14.2.0_2014.06.13 and 14.0.17_2014.06.09 , the > lower panel of Console from JSmol applet is write protected, i.e. can’t > type commands to

Re: [Jmol-users] JSmol write protected Console?

Yes, I think I saw that yesterday, while I was testing several versions for chasing another problem, so I'm not sure which one it was. But it sound like the same. El 18 Jun 2014 a las 10:32, Jaime Prilusky escribió: > >From my server with Jmol 14.2.0_2014.06.13 and 14.0.17_2014.06.09 , > the

[Jmol-users] JSmol write protected Console?

>From my server with Jmol 14.2.0_2014.06.13 and 14.0.17_2014.06.09 , the lower >panel of Console from JSmol applet is write protected, i.e. can’t type >commands to be executed. On Jmol 14.1.16 it was Ok. Can others reproduce this? Jaim * 14.2.0_2014.06.1 ---

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

[Jmol-users] jsmol wordpress plugin

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 deployed it on EcoliWiki. The main reason for joining is

Re: [Jmol-users] JSmol 14 open/save dialogs freezes

This box is entirely controlled by your browser. Jmol has no control over it. My experience is that sometimes the box can be slow to come up and appear to be stalled because the default directory has a very large number of files or because, in my case at least, a network drive that has not been dis

[Jmol-users] JSmol 14 open/save dialogs freezes

Hello everyone, JSmol open/save dialog boxes freezes often showing a blank dialog boxes with no options. Why does this happen!, How can I prevent it from freezing all the time, I have to restart the browser, but that's annoying designing a complete view and unable to save the molecule as imag

Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

Eric, make sure you have both newer JSmol.min.js and j2s directory. On Mon, Apr 14, 2014 at 7:30 PM, Robert Hanson wrote: > Let's see what we can find here: > > > jmolApplet0._applet.viewer.global.disablePopupMenu > true > > so something happened there. That flag is set in viewer: > > private

Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

Let's see what we can find here: jmolApplet0._applet.viewer.global.disablePopupMenu true so something happened there. That flag is set in viewer: private Object getPopupMenu() { if (jmolpopup == null) { jmolpopup = (allowScripting ? apiPlatform.getMenuPopup(menuStructure, 'j') : nul

Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

Anyway, that's still quite old. We are up to 14.0.13. On Mon, Apr 14, 2014 at 7:13 PM, Robert Hanson wrote: > Right, sorry. Looked at the wrong line: > > Jmol Version: 14.0.4 2014-01-05 16:16: > java.vendor: j2s > java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM > > > > > On Mon, Apr 14, 2014

Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

Right, sorry. Looked at the wrong line: Jmol Version: 14.0.4 2014-01-05 16:16: java.vendor: j2s java.version: JSmol 13.3.9 11/23/2013 10:51:10 PM On Mon, Apr 14, 2014 at 6:56 PM, Eric Martz wrote: > Hi, Bob, > > As stated below, I am already using 14.0.4 in the released version of > FirstGlan

Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

Hi, Bob, As stated below, I am already using 14.0.4 in the released version of FirstGlance 1.98 (firstglance.jmol.org, uncheck the Java checkbox and enter a PDB code). Also when I use 14.0.13 (running in Firefox from local files) I can't get the menu to open. Regards, Eric At 4/14/14, Robert

Re: [Jmol-users] JSmol menu doesn't open in FirstGlance

Try upgrading to Jmol 14.0. On Sun, Apr 13, 2014 at 5:06 PM, Eric Martz wrote: > I cannot seem to get the JSmol menu to open (14.0.4): > > http://firstglance.jmol.org/fg.htm?mol=1d66&use=html5 > > For comparison, the menu opens just fine with the Java applet: > > http://firstglance.jmol.org/fg.h

[Jmol-users] JSmol menu doesn't open in FirstGlance

I cannot seem to get the JSmol menu to open (14.0.4): http://firstglance.jmol.org/fg.htm?mol=1d66&use=html5 For comparison, the menu opens just fine with the Java applet: http://firstglance.jmol.org/fg.htm?mol=1d66 I have the same problem with JSmol 14.0.13 in local testing. Is JSmol too close

Re: [Jmol-users] JSmol Lite and PDB files?

On Tue, Mar 18, 2014 at 2:48 PM, tinus updates wrote: > Thank you all! > > I have understood that Jmol.getTMApplet uses JSmol.lite.js or > JSmol.lite.nojq.js. So I adapted the lite4.htm file provided in the > distribution. The other liteX.htm files did not work "out of the box", so I > left them a

Re: [Jmol-users] JSmol Lite and PDB files?

Martin, > replaced with the correct sz/ice.pdb. Please try src: "load sz/ice.pdb", instead of src: "sz/ice.pdb", > I wonder by the way if a bigger molecule or structure is displayed clearly > enough with the limited > rendering. Bigger is not the issue (althugh i may respond slowly). Limit

Re: [Jmol-users] JSmol Lite and PDB files?

Thank you all! I have understood that Jmol.getTMApplet uses JSmol.lite.js or JSmol.lite.nojq.js. So I adapted the lite4.htm file provided in the distribution. The other liteX.htm files did not work "out of the box", so I left them aside. Robert, I found your quoted code in js/JSmol.full.lite.js a

Re: [Jmol-users] JSmol Lite and PDB files?

proto._parse = function(data) { // just MOL data for now this._parseSDF(data); } On Tue, Mar 18, 2014 at 10:59 AM, tinus updates wrote: > If I set the src: (or script: "load ...") field in the Info variable to > load anything other than a MOL file, there is nothing displayed: > > www.per

Re: [Jmol-users] JSmol Lite and PDB files?

Also, you won't be able to read a binary file (.gz) with JSmol.lite.nojq.js. It is VERY light On Tue, Mar 18, 2014 at 10:59 AM, tinus updates wrote: > If I set the src: (or script: "load ...") field in the Info variable to > load anything other than a MOL file, there is nothing displayed: >

Re: [Jmol-users] JSmol Lite and PDB files?

Hi Martin You need to read carefully the instructions. You are trying the lightweight object, with getTMApplet, but that does not use JSmol.min.js but the special JSmol.lite.js and not all Info parameters are supported and even if "src" was supported, it must be a script of commands, not a filen

Re: [Jmol-users] JSmol Lite and PDB files?

If I set the src: (or script: "load ...") field in the Info variable to load anything other than a MOL file, there is nothing displayed: www.permafrost.ch/jsmol/eis-lite.htm (code from lite4.htm) The "normal" Jmol.getAppletHtml works fine, though: www.permafrost.ch/jsmol/eis.htm Sorry if I lack

Re: [Jmol-users] JSmol Lite and PDB files?

On Mon, Mar 17, 2014 at 4:11 PM, tinus updates wrote: > Hi, > I want to show some structures to my students on iPad 2. Somehow I can > only get small MOL files to display, no PDB files. Is there a list of > supported file formats? The "normal" JSmol works just fine, but is slow on > iPad. > Thanks

[Jmol-users] JSmol Lite and PDB files?

Hi, I want to show some structures to my students on iPad 2. Somehow I can only get small MOL files to display, no PDB files. Is there a list of supported file formats? The "normal" JSmol works just fine, but is slow on iPad. Thanks! Martin --

Re: [Jmol-users] Jsmol fails to load the pdb file in Chrome, works in Firefox

I would start by upgrading to Jmol 14.1.8 from Jmol 13.2.7 http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.8_2014.02.08.zip 13.2.7 is ages ago! Many many improvements since last July... On Fri, Feb 7, 2014 at 1:43 PM, Dina Schneidman wrote: > Thanks, I removed ".zip" and it started working.

Re: [Jmol-users] Jsmol fails to load the pdb file in Chrome, works in Firefox

Thanks, I removed ".zip" and it started working. Is there a way to speed up the load time? It takes ~20+ second to load it: http://modbase.compbio.ucsf.edu/foxs/cgi/showRes2.pl?dirname=pdbfiles_38_22_11_7_1_114&profileFileName=x140xlf.dat On Wed, Feb 5, 2014 at 8:04 AM, Robert Hanson wrote: > th

Re: [Jmol-users] Jsmol fails to load the pdb file in Chrome, works in Firefox

the ".zip" in the file name is almost certainly telling JSmol that this is a zip file and thus binary. Jmol/Java doesn't care, but JSmol/HTML5 does. And Chrome is the one that would be affected. So either (1) change that file signature to not include zip or (2) add a JavaScript line after you loa

[Jmol-users] Jsmol fails to load the pdb file in Chrome, works in Firefox

Hi, I have converted Jmol to Jsmol using adapter library. All works well in Firefox, however for Chrome I get an error message: "unrecognized file format for file ..." Here is a link to the page: http://modbase.compbio.ucsf.edu/foxs/cgi/showRes2.pl?dirname=pdbfiles.zip_23_19_14_30_0_114&profileFi

Re: [Jmol-users] JSmol broken on Mac Safari back button

Otis, Thank you for the suggestions. Looking into that, Jaim On Jan 30, 2014, at 8:46 PM, Otis Rothenberger mailto:osrot...@chemagic.com>> wrote: Jaim, I see the same thing you are seeing on Bob's page. But... Interesting point: I don't see any of this problem on my site - Safari, cross dom

Re: [Jmol-users] JSmol broken on Mac Safari back button

Jaim, I see the same thing you are seeing on Bob's page. But... Interesting point: I don't see any of this problem on my site - Safari, cross domain or within domain: http://chemagic.com/JSmolVMK2.htm After above load, location box = chemagic.com followed by back button reloads JSmol The onl

Re: [Jmol-users] JSmol broken on Mac Safari back button

Thank you for the additional testing and suggestions. I tested now on Chrome Version 32.0.1700.102, same Mac, and it works great: no freezing. I had the idea that Safari and Chrome shared a lot of internal code, but it seems that their behaviour with objects is different. The freezing, of cours

Re: [Jmol-users] JSmol broken on Mac Safari back button

Jaim, I see what you're seeing with Safari. Just to add a data point to the discussion, when I use the location box to navigate to another site (e.g. Google.com), the back button does force a reload of JSmol on your page. When I try this same location box approach with: http://proteopedia.org

Re: [Jmol-users] JSmol broken on Mac Safari back button

On 01/30/2014 01:11 PM, Philip Bays wrote: > Two comments: > I thought that the Safari behavior was the normal for the back button. I > hate it when I am reading and article, click a link to another page, and then > when I come back to the original, the page reloads and I have to search for >

Re: [Jmol-users] JSmol broken on Mac Safari back button

Two comments: I see the difference that you do except that the applet works fine in Safari when I come back to the page. That is, I do not see a broken applet, it is just not refreshed. (Mac OS 10.9.1) I thought that the Safari behavior was the normal for the back button. I hate it when I

[Jmol-users] JSmol broken on Mac Safari back button

Is there a way to force loading JSmol when loading/rendering a page? JQuery should be able to do this. This is why we might need to start with a fresh loaded JSmol: When clicking a ‘back to previous page’ button on On Mac 10.9.1, Safari 7.0.1, JSmol renders non-operational. On Firefox 26.0, sam

Re: [Jmol-users] JSmol and jquery.simplemodal.1.4.4.min.js

Jmol.getAppletHtml("jmolApplet0", Info) is fine. It is defined as: // optional Info here Jmol.getAppletHtml = function(applet, Info) { if (Info) { var d = Jmol._document; Jmol._document = null; applet = Jmol.getApplet(applet, Info); Jmol._document = d; } re

Re: [Jmol-users] JSmol and jquery.simplemodal.1.4.4.min.js

Hi, Carlo (?) I cannot help much with jQuery, but you should not be using that syntax jmolButton('spin on','spin it!'); but instead Jmol.jmolButton(jmolApplet0, 'spin on','spin it!'); (The first one may work if you are using Jmol2.js, but since you have these errors I think it's better to go f

Re: [Jmol-users] JSmol and jquery.simplemodal.1.4.4.min.js

Hi! Thank you very much for your attention and help ! Actually no error is generated if I'm using jQuery in this way: $("#visualize_tensor_display").append(Jmol.getAppletHtml("jmolApplet0",Info)); The problem occurs when I try to do this: $("#visualize_tensor_commands").append("jmolButton('spi

Re: [Jmol-users] JSmol and jquery.simplemodal.1.4.4.min.js

I'd say congratulations are in order for just getting the protein there! :) My guess is that you will see some sort of JavaScript error in the JavaScript console. What happens when you debug this with the developer console open or with the debugger running? Debugging jQuery can be a real challen

[Jmol-users] JSmol and jquery.simplemodal.1.4.4.min.js

Hi to everyone !! I tried to realize a kind of dialog window using Jquery Simplemodal in which I would like to create a simple Jmol interface showing the proteins and with some buttons for different actions. It is not the first time that I implement an interface using Jmol/JSmol and everything was

[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] jsmol and dropdowns

You will need to increase the z-order of the dropdowns to > 1 or you can manually change the setting of Jmol.z in Jmol.min.js from its current setting of 9000 On Tue, Jan 14, 2014 at 10:04 AM, Richard Steane < richard.ste...@ntlworld.com> wrote: > *Hello Bob and co* > > *Having converted

[Jmol-users] jsmol and dropdowns

Hello Bob and co Having converted most of my old Jmol pages to use jsmol, I note that dropdown menus annoyingly fall “behind” the molecule display area, if using jsmol14. I don’t think it happened with jsmol13 (unless you switch to JMol and back again to HTML5). All the files accessible from

Re: [Jmol-users] jsmol problems

The message is saying that the applet by that name does not exist. I think that was done in the older Jmol.js was to indicate the applet by just its suffix: "1" in this case: jmolScript(s, “1”); not jmolScript(s, “jmolApplet1”); So that should be the only problem. By the way, you don't hav

Re: [Jmol-users] jsmol problems

can you send me that page, so I can look at it? On Mon, Jan 13, 2014 at 10:11 AM, Spinney, Richard < rspin...@chemistry.ohio-state.edu> wrote: > > > > function sync2() { > > > var syncing = document.getElementById("drive").checked > > > var s = (syncing ? 'sync * off;sync . on;sync jmolAppletB o

Re: [Jmol-users] jsmol problems

> function sync2() { > var syncing = document.getElementById("drive").checked > var s = (syncing ? 'sync * off;sync . on;sync jmolAppletB on;sync jmolAppletB > "set syncMouse on;set syncScript off";': 'sync * off') jmolScript(s, > "A"); } > > So the script is being sent to jmolAppletA, and

Re: [Jmol-users] jsmol problems

Rick, be sure you are using yesterday's Jmol release -- One of the recent fixes had to do with synchronization. But I guess if it is working, there should be no problem. I have put up a file, http://chemapps.stolaf.edu/jmol/jsmol/sync4.htm, which you can use for testing. There's a link there "just

Re: [Jmol-users] jsmol problems

Rick, I can help you with #1. The following makes it go away: Jmol._alertNoBinary = false; jmolApplet0 = Jmol.getApplet("jmolApplet0", Info); Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com On Jan 10, 2014, at 1:32 PM, Spinney, Richard wr

[Jmol-users] jsmol problems

I have been working on some "new" jsmol stuff and have run into a few problems. 1) I get an alert when using HTML5: "JmolCore.js: synchronous binary file transfer is requested but not available." Click ok and it works fines so I am not sure why this alert is showing up. There are no error

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] JSmol menu doesn't open

Are you in any way disabling or capturing events from mouse right-click ? Jaim On Jan 7, 2014, at 5:56 PM, Eric Martz wrote: > I cannot seem to get the JSmol menu to open in 14.0.3 e.g. > > http://firstglance.jmol.org/fg.htm?mol=1d66&use=html5 > > Any suggestions? > > Eric > > > > >

[Jmol-users] JSmol menu doesn't open

I cannot seem to get the JSmol menu to open in 14.0.3 e.g. http://firstglance.jmol.org/fg.htm?mol=1d66&use=html5 Any suggestions? Eric -- Rapidly troubleshoot problems before they affect your business. Most IT organ

Re: [Jmol-users] JSmol popup menu on an iPad

Bob: That works but the positioning is sometimes barely visible and the menu links do not work at all on an iPad. J. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Norte Dame, IN Sent from my iPad > On Dec 27, 2013, at 1:15 PM, Bob Hanson wrote: > > Doesn't clicking on the

Re: [Jmol-users] JSmol popup menu on an iPad

Doesn't clicking on the logo work? Sent from my stupid iPhone On Dec 25, 2013, at 12:31 AM, "Rzepa, Henry S" wrote: > 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

Re: [Jmol-users] JSmol popup menu on an iPad

The menu command will bring up the menu, but be careful. The command must be just "menu" - no trailing space or CR/LF caused by using [enter] in the console. The latter will throw an error. The bad news on an iPad is that the resulting menu does not respond to touches. Otis -- Otis Rothenberge

[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] JSmol bug?

Hmm. That's odd. I was sure I got that right, and it is correct on my installation. -- one says Jmol 14.0.2 and the other Jmol 14.1.2. In reality they are the same. Neither should be showing a "dev" version. You sure you got that at http://sourceforge.net/projects/jmol/files/ ? I just downloaded t

[Jmol-users] JSmol bug?

I have just installed version 14.0.2 (after trying 14.1.2) and both state that they are 14.1.1_dev_2013.12.12. It seems to have problems with the remarks line in a PDB file (failing to load the molecule), and in JSmol I get the error message that JmolCore.js in unavailable, I assume it should be

Re: [Jmol-users] JSmol HTML5 code : remaining

In JSmolCore.js it reads: if (isHeader) { ... s = "\ ...IMG\ .."; ... } else { s = "\ ..\ ..\ ..\ .[x]\ .\ ..\ ..."; Pretty sure those are all balanced. Bob On Thu, Dec 12, 2013 at 10:04 AM, Robert Hanson wrote: > should be a first half o

Re: [Jmol-users] JSmol HTML5 code : remaining

should be a first half of that as well. That's the footer. On Wed, Dec 11, 2013 at 11:59 PM, Paul Pillot < paul.pil...@ac-orleans-tours.fr> wrote: > 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,

[Jmol-users] JSmol HTML5 code : remaining

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 : "[x]NCI(small molecules)PubChem(small molecules)RCSB(macr

Re: [Jmol-users] JSmol for testing....

Bob: I privately sent you some error messages earlier this morning. Did you get the email? I have a Safari 7.0 update As I reported in that prior message, jsmol.htm does not load the applet from your site. I have put a copy of the jsmol directory on my campus server. The applet in jsmol.ht

Re: [Jmol-users] JSmol for testing....

Thanks, Phil. I left "/jsmol" out of a bunch of those links; the download link is right. (Isn't it nice to have trusted-signed applets? Perhaps we will soon forget the days of all those warning messages.) By the way, at least for me, Chrome and MSIE are working for non-binary file formats on local

Re: [Jmol-users] JSmol for testing....

Bob: I think that your links here are not correct. And is the download link right?? Sent from my iPad > On Dec 1, 2013, at 9:05 PM, Robert Hanson wrote: > > again! http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.01.zip > > http access tests : > > http://chemapps.stolaf.edu/jmol/jsm

[Jmol-users] JSmol for testing....

again! http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.12.01.zip http access tests : http://chemapps.stolaf.edu/jmol/jsmol.htm http://chemapps.stolaf.edu/jmol/jsmol.htm?_USE=SIGNED http://chemapps.stolaf.edu/jmol/jsmol.htm?_USE=JAVA loading caffeine loading 1hxw loading Pymol session loadi

Re: [Jmol-users] JSmol Problems

that upload did not address that issue. Fixed in next On Wed, Nov 27, 2013 at 4:25 PM, Philip Bays wrote: > Bob: > The bondset issue is still there when running locally from the ….27 > directory. > > > > On Nov 27, 2013, at 4:44 PM, Robert Hanson wrote: > > http://chemapps.stolaf.edu/jmo

Re: [Jmol-users] JSmol Problems

OK, jmol-13.3.9_2013.11.27 is uploaded. The right click menu now comes up, but it's reporting jmol-13.3.9_2013.11.26 - Chrome, Safari, and FF. Cache cleared on all to the extreme. Safari still does not load, but... It will load if I have the error console up - no errors reported. With Safari, Chr

Re: [Jmol-users] JSmol Problems

Bob: The bondset issue is still there when running locally from the ….27 directory. On Nov 27, 2013, at 4:44 PM, Robert Hanson wrote: > http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27.zip > > fixes the bondset problem. > > How do I get to your site to test this? > > > > > O

Re: [Jmol-users] JSmol Problems

Sorry about that: http://chemistry.illinoisstate.edu/osrothen/JSmolVMK.htm Also a new interface that we're developing: http://chemistry.illinoisstate.edu/osrothen/JSmolVMK2.htm Chrome is now working on some loads, but it breaks after some playing around. Also check out the inability to bring up

Re: [Jmol-users] JSmol Problems

http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.27.zip fixes the bondset problem. How do I get to your site to test this? On Wed, Nov 27, 2013 at 2:16 PM, Otis Rothenberger wrote: > I apologize in advance for starting a new thread here, but I'm getting > really confused on issues. My

[Jmol-users] JSmol Problems

I apologize in advance for starting a new thread here, but I'm getting really confused on issues. My focus here is this note from Bob this morning. >From Bob... OK. Tomorrow is Mac-testing day for me. Tell me your woes Please do try the latest, at http://chemapps.stolaf.edu/jmol/zip/jmol-1

[Jmol-users] JSmol - Firefox

I'm also seeing the missing BondSt.js warning in the Opera developers console with JSmol (from Jmol-13.3.9_2013.11.25d) though JSmol still displays with Opera and Chrome. However. I'm finding display with Firefox is inconsistent, usually showing a blank JSmol instance, though on repeated refresh,

Re: [Jmol-users] JSmol load monitor translucency

Jmol._j2sLoadMonitorOpacity On Mon, Nov 25, 2013 at 12:31 PM, Robert Hanson wrote: > Can I just expose the default opacity? What it does is drop the opacity by > 5 every 40 ms, so all you have to do is set it at some high number -- like > 200 -- to have one full second of full opacity. > > > O

Re: [Jmol-users] JSmol load monitor translucency

Can I just expose the default opacity? What it does is drop the opacity by 5 every 40 ms, so all you have to do is set it at some high number -- like 200 -- to have one full second of full opacity. On Mon, Nov 25, 2013 at 12:19 PM, Rolf Huehne wrote: > On 11/25/2013 07:04 PM, Angel Herráez wrot

Re: [Jmol-users] JSmol load monitor translucency

On 11/25/2013 07:04 PM, Angel Herráez wrote: > I see, Bob > So the opacity is being changed by the running code. That's why > setting it fixed in CSS prevents it from disappearing --apart from > killing the 'loading' effect. > I think this "fix" is quite messy. I would not play with it, Rolf. > May

Re: [Jmol-users] JSmol load monitor translucency

I see, Bob So the opacity is being changed by the running code. That's why setting it fixed in CSS prevents it from disappearing --apart from killing the 'loading' effect. I think this "fix" is quite messy. I would not play with it, Rolf. Maybe if you just change to another background color it w

Re: [Jmol-users] JSmol load monitor translucency

On Mon, Nov 25, 2013 at 10:35 AM, Angel Herráez wrote: > > That would be tricky to do without going into the JSmol code > > and changing it directly. Do so only if you do not worry about future > > JSmol updates. > > It should be possible to chenge that using a CSS rule that overrides > what is se

Re: [Jmol-users] JSmol load monitor translucency

> Thanks, Angel. That does the trick. But now the last message > "Application loaded." stays visible until the mouse is moved over the > message. Shouldn't happen, unless the source code is playing with the opacity at the end instead of removing the element of hiding it using 'display'. Don't

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