probably a caching problem.
On Thu, Feb 26, 2015 at 8:31 AM, Spinney, Richard <
rspin...@chemistry.ohio-state.edu> wrote:
> I have a multi-model PDB file that ran fine with version 12 but fails
> with version 14.3.12 2.22.2015 with an error message of “ERROR creating
> model: TypeError: this.jbr
I have a multi-model PDB file that ran fine with version 12 but fails with
version 14.3.12 2.22.2015 with an error message of "ERROR creating model:
TypeError: this.jbr is null" Is this an issue with the file or is there a bug
in this version?
Thanks, Rick
--
, although another has popped
up but I’ll start a new thread.
All the best,
Anthony
From: Otis Rothenberger [mailto:osrot...@chemagic.com]
Sent: 19 January 2015 14:36
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Error message in Chrome but not in Firefox or IE
Anthony,
There may be
Anthony,
There may be problems in that error report that I'm not seeing, but one
thing I will point out is that Chrome requires a terminal start-up (at
least on the Mac) to run files locally. It's a pain, but you have to start
from the terminal (Mac) with:
open -a /Applications/Google\\ Chrome.ap
All,
I'm experiencing an error that is probably simple to fix but I'm lost. I'm
trying to create a simple page, based upon the test2.htm example. Both the
original test2 file (slightly edited to work locally) and the simplified one
I've created work in Firefox and IE but an error is thrown by C
that's what I needed. Thanks.
Bob
On Sat, Jan 12, 2013 at 2:14 PM, Otis Rothenberger wrote:
> var mol = "string";
> var version = Jmol.getPropertyAsArray(jmolApplet0, "appletInfo.version")
> var c = new Date();
> mol += "\n__Jmol-" + version.substring(0,2);
> mol += String("_0" + (1 + c.getMonth
Bob,
Some naiveté on my part here: I had to use my specific object jmolApplet0. I do
not know how to translate the object Viewer to JavaScript. Also, I don't
understand the final Escape.escape(bs). I'll avoid explicitly stating the
obvious laugh line on this latter point. Jmol returns the first
Bob,
I get the basic flow of what's happening below, so I'll try. My JavaScript is
pretty primitive and chaotic, so you'll have considerable clean up to do!
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Jan 11, 2013, at 10:47 AM, Robert Hanson wrote:
> That will take a bi
That will take a bit of work. I seem to have missed that. What we are doing
there is setting up the MOL file date line. Maybe you can help me by
writing the JavaScript equivalent of this:
StringXBuilder mol = new StringXBuilder();
String version = Viewer.getJmolVersion();
Calendar
Bob,
With JSmol, I'm getting an error message that I don't understand. I'm getting
the same message in different contexts:
TypeError: 'undefined' is not an object (evaluating
'java.util.Calendar.getInstance') 58490
http://chemagic.com/JSmol/j2s/core/core.z.js
Most recently, I get this with:
Laurent, are you sure youhave the whole set of jar files in the server? If it
works with
jmolAppletSigned.jar and not with jmolAppletSigned0.jar, it sounds like that
may be the key.
As Bob said, you better use Jmol.js. That will invoke *0.jar, so the comment
still aplies
--
Well, you probably can't load PDB files from the RCSB using the unsigned
applet. So that's where I would wonder. Please use Jmol.js.
On Thu, Apr 28, 2011 at 8:00 AM, Laurent Gil wrote:
> Hi,
>
> I installed Jmol in a web server and it works very well when I use local
> PDB files.
> But when I tr
Sorry, I found the solution:
I replaced
by
Laurent
On 28/04/2011 14:00, Laurent Gil wrote:
> Hi,
>
> I installed Jmol in a web server and it works very well when I use local
> PDB files.
> But when I try to use URL, the message "File reader was not found:Pdb"
> in the applet.
>
> I see thi
Hi,
I installed Jmol in a web server and it works very well when I use local
PDB files.
But when I try to use URL, the message "File reader was not found:Pdb"
in the applet.
I see this message if I use the JavaScript library or the ""
method, on both windows 7 and linux ubuntu machines (with t
Bob, i moved the applet and code to my other site and it seems working
http://pinostriccoli.altervista.org/?p=1094
I used the code that you suggested me (
)but always with applet tag, then i used the usual code and it seems
working now.
In this different site, i uploaded all Jmol files and fil
Bob,
In order to insert the applet, i use tag, since i have always
troubles with javascript. But why i dont have any problem accessing the
site from my mac laptop ?
I added the code you suggested me and it loads fine but errors are
there. Can it be with some error on java local engine?
Tomorr
Are you hardcoding the applet tag? I think maybe you are. Try using the
JmolApplet()
command instead and see if that fixes it. It's happening for me as well at
your site, but all the file references look fine. So it's definitely
something about that site.
You might also try removing the load par
Dear friends, lately i had an error message on the following page
http://digilander.libero.it/industrialegalilei/organica/rx/sn2.htm
when, after downlading the page, i try to click on one of three buttons
below floruro, bromuro ioduro.
This error appears in Firefox and google and IE in windows xp
FABULOUS! This will be quite valuable, I'm sure. Thank you, Francois!
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to
Dear Jmol users,
To conclude. thanks to all.
regards, Francois
Help about installing the Java Runtime Environment (JRE from Sun)
on 64 bits RedHat-based Linux (CentOS 5.4 & Fedora 12) distributions
Opera 10.11, Firefox 3.5.11 and Chrome 5.0.375.125 under linux are
used with Java applets to d
Quoting Robert Hanson :
> well, then that particular implementation of Opera has a bug, doesn't it?
ok, fine for me ;-)
> Jmol.js is automatically indicating "." for the path when JmolInitialize()
> is missing. And since vibrate.htm is working, then that is definitely not
> the problem. The "sim
well, then that particular implementation of Opera has a bug, doesn't it?
Jmol.js is automatically indicating "." for the path when JmolInitialize()
is missing. And since vibrate.htm is working, then that is definitely not
the problem. The "simplified" page you have there loads for me. But you are
Dear Bob,
I made some progresses. I will summarize to the Jmol mailing when finished.
See http://q4md-forcefieldtools.org/RED/popup/javaconfig.php
The applet @ http://q4md-forcefieldtools.org/RED/popup/javaapplet.php
works fine using Firefox 3.5.11 & Chrome 5.0.375.125 under fedora 12.
However,
I don't think that is correct. Not sure what "$path" is all about -- were
you just putting that in there in place of what it really is?
Opera does not require jmolInitialize any more than the other browsers. At
least in my hands. What is your observation, and what version of Opera?
http://chemapp
Dear Bob,
> try
> jmolInitialize("$path/jmol", "JmolApplet.jar");
It looks like jmolInitialize("$path/jmol", "JmolApplet.jar"); is
required for Opera but not for Firefox and Chrome.
Do you know why ?
thanks, regards, Francois
How are you launching the browser? Are you typing "firefox" on a command
line or clicking on a toolbar icon?
I have run into situations where there is more than one version of the
browser installed on my CentOS machine (aka, RHEL) and the two methods point
to different installations. Firefox lin
Quoting Matthew Betts :
> Did you enable the plugin with the final step mentioned on the jmol wiki?:
>
> open Firefox, select Tools > Addons, and enable the Java plug-in
I cannot because it is not found.
> You may also need to disable the IcedTea plugin (which uses openjdk)
> from the same men
Hi,
Did you enable the plugin with the final step mentioned on the jmol wiki?:
open Firefox, select Tools > Addons, and enable the Java plug-in
You may also need to disable the IcedTea plugin (which uses openjdk)
from the same menu.
> - should I install jre 1.6.x or 1.5.x from sun ?
I inst
Dear Matthew & Jmol users,
> This sounds like the same error that I had recently on Fedora 11. It
> comes with OpenJDK by default but you need to uninstall that and
> install the one from Sun, along with the associated plug in for
> firefox. Please see my most recent post, and/or you might have to
try
jmolInitialize("../jmol", "JmolApplet.jar");
just to see if the implementation of Java is having problems with
progressive class loading.
On Fri, Jul 23, 2010 at 7:15 AM, FyD wrote:
> Dear Jmol users,
>
> I can display the following applet:
> http://jmol.sourceforge.net/demo/atoms/
> un
Matthew Betts wrote:
> Please see my most recent post, and/or you might have to ask
> your IT Support for help (I found it a bit tricky anyway).
That's now also at
http://wiki.jmol.org/index.php/Troubleshooting/Applet#The_applet_is_di
splayed.2C_other_problems
---
Hi,
This sounds like the same error that I had recently on Fedora 11. It
comes with OpenJDK by default but you need to uninstall that and
install the one from Sun, along with the associated plug in for
firefox. Please see my most recent post, and/or you might have to ask
your IT Support for help (
Dear Jmol users,
I can display the following applet: http://jmol.sourceforge.net/demo/atoms/
under windows xp(firefox) & linux(fedora 12, 64 bits; firefox 3.5.10)
without any problem.
Now when create my applet (very basic) using caffeine.xyz @
http://molmodel5.sa.u-picardie.fr/~red/x/javaapplet
Thanks! it works when I use load cube command.
On Wed, Nov 5, 2008 at 3:15 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> One of the problems with cube files is that they do not have much in the way
> of characteristic information. You can force cube file reading using:
>
>
> load cube::filename
>
One of the problems with cube files is that they do not have much in the way
of characteristic information. You can force cube file reading using:
load cube::filename
I'd be interested in seeing the offending file.
On Wed, Nov 5, 2008 at 1:57 PM, Yi Mao <[EMAIL PROTECTED]> wrote:
> I was using
I was using jmol to generate surface based on gaussian output. The
guassian output is in *.cube format. It works fine with most molecules
except one case. I followed the same procesure as other molecules to
generate the cube file, however, jmol failed to open it.
The error message reads "
"script
ile
3LDH appears as a monomer even with the complete header.
In any case, I have solved my problem. There is probably an issue of the
file format.
Thanks,
-Steve
Message: 2
Date: Thu, 15 Mar 2007 08:26:45 -0500
From: Bob Hanson <[EMAIL PROTECTED]>
Subject: [Jmol-users] Error message- C
file
3LDH appears as a monomer even with the complete header.
In any case, I have solved my problem. There is probably an issue of the
file format.
Thanks,
-Steve
Message: 2
Date: Thu, 15 Mar 2007 08:26:45 -0500
From: Bob Hanson <[EMAIL PROTECTED]>
Subject: [Jmol-users] Error message-
34 -0500
From: Steven Vik <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Subject: [Jmol-users] Error message- Cannot invert matrix
To: < jmol-users@lists.sourceforge.net
<mailto:jmol-users@lists.sourceforge.net>>
Message-ID: <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECT
Using both the applet and the application ( jmol-11.0.RC4), I get the
following error message when using the pdb file 6LDH:
ScriptException:javax.vecmath.SingularMatrixException: cannot invert matrix
Presumably there is something unusual about this pdb file, but I can't
figure out what it is.
-S
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