On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson hans...@stolaf.edu wrote:
Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is still
work to be done to ensure faithful rendition, but it's a start.
Nice!
Do you also have in mind of writing such files? That would very nicely
Hi,
I'm trying to switch my JMol applet web page to JSMol - mainly to avoid all
the problems related with ever increasing restrictive security policies for
Java. I put all the main JSMol files in a folder, j2s in a subfolder,
loaded the scripts:
script type=text/javascript
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 :
Tried that. Every other order either increases the number of error
messages, or leaves the situation unchanged.
2013/2/22 Paul Pillot paul.pil...@ac-orleans-tours.fr
Order matters in your js files links
I use the following declaration:
script type=text/javascript src=jmol/JSmol.min.js/script
Hello Simone
#1
I believe (but am not sure) that with the latest versions you only
need to call JSmol.min.js
The call to j2sjmol.js will be done internally based on the path
specufied in the Info variable.
#2
Information in the Wiki is not up-to-date (must find time to do it,
and the WIki was
Ah, OK
JSmol distribution is still not well roganized, I'm afraid. There's
also a bit of confusion between Jmol-JSO and JSmol (which I'm
planning to sort out and explain in the wiki)
I suggest that you download from StOlaf. The link is in the wiki
http://wiki.jmol.org/index.php/JSmol
(there
I used the new package and, as suggested, included only the JSmol.min.js
script file. The result is a very similar error message, which now I can't
manage to reproduce because Firefox keeps simply getting stuck when I try
to load the page. I also lose all jQuery UI functionality that I had
Ok, the error message came up again, it's:
2013/2/22 Simone Sturniolo simonesturni...@gmail.com
I used the new package and, as suggested, included only the JSmol.min.js
script file. The result is a very similar error message, which now I can't
manage to reproduce because Firefox keeps
Sorry, it seems like the mail was sent by mistake. The error message:
TypeError: b._getElement(...).style is undefined
...!c(this._isInfoVisible=c,this._infoObject?this._infoObject._showInfo(c):b._get...
JSmol.min.js (line 236)
2013/2/22 Simone Sturniolo simonesturni...@gmail.com
Ok, the
I know ^^, I sent another email right after that, sorry for the mistake!
2013/2/22 N David Brown hubd...@gmail.com
You didn't list the error :-)
On 22 February 2013 15:07, Simone Sturniolo simonesturni...@gmail.comwrote:
Ok, the error message came up again, it's:
2013/2/22 Simone
On Fri, Feb 22, 2013 at 3:49 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson hans...@stolaf.edu wrote:
Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is
still
work to be done to ensure faithful rendition, but it's a
If you send me a copy of the page or a link to it, I can help you track
this down. Something simple, I'm sure.
On Fri, Feb 22, 2013 at 6:46 AM, Simone Sturniolo simonesturni...@gmail.com
wrote:
Tried that. Every other order either increases the number of error
messages, or leaves the
-Original Message-
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: Fri 2/22/2013 11:59 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 13.1.13 released - several new features
On Fri, Feb 22, 2013 at 3:49 AM, Egon Willighagen
egon.willigha...@gmail.com
It's a bit of a big thing. 5 MB at least I'd say, all things included. How
do you prefer me to send it?
Simone
2013/2/22 Robert Hanson hans...@stolaf.edu
If you send me a copy of the page or a link to it, I can help you track
this down. Something simple, I'm sure.
On Fri, Feb 22, 2013 at
email is fine. I have time today to look at it. I'm sure it will only take
a few minutes.
On Fri, Feb 22, 2013 at 11:53 AM, Simone Sturniolo
simonesturni...@gmail.com wrote:
It's a bit of a big thing. 5 MB at least I'd say, all things included. How
do you prefer me to send it?
Simone
Does anybody know about a JSmol version of WebMO? We're going to have trouble
doing computational chemistry experiments in our teaching labs without Java,
since we use WebMO. I would appreciate any information or insights anybody can
offer. Thanks.
Jennifer
Jennifer L. Muzyka
Professor
Jennifer,
Looks like the last update to WebMO was in August 2012. Perhaps a version
employing JSMol is in the works? Not sure. I don't see any reason why it
shouldn't be possible...Jmol just reads the output of WebMO calculations;
it doesn't do any of the calculations itself.
BTW, I lived at
No sign of that yet.
Is there a reason you do not have Java in your teaching labs? Is this just
an IT department crack-down? St. Olaf is still supporting Java
On Fri, Feb 22, 2013 at 12:08 PM, Jennifer L. Muzyka
jennifer.muz...@centre.edu wrote:
Does anybody know about a JSmol version of
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 Object. I'm happily running scripts with
something like
var script = lots of commands;
Jmol.script (myJmol1,
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
var q = Jmol.evaluate(myJmol, quaternion())
On Fri, Feb 22, 2013 at 1:27 PM, Dan Kirshner dan_kirsh...@yahoo.comwrote:
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
Bob,
Java has been disabled on all campus computers at Centre. I think Centre's
response is pretty reasonable, given that Homeland Security recommends
disabling Java. See the article the ITS folks shared with me:
Mike,
Thanks for checking on the latest WebMO update. I contacted them and they say
there's no way all that complex Java stuff can be done with JavaScript. On my
reply, I copied Bob Hanson. He responded with details about JSmol that will
hopefully get the WebMO folks thinking about the
sure, but
quaternion()
should do the same thing -- and we should think about the fact that with
JSmol we don't need conversion from Java classes, since everything is
JavaScript!
Bob
On Fri, Feb 22, 2013 at 1:51 PM, Paul Pillot
paul.pil...@ac-orleans-tours.fr wrote:
Java is back working on Safari. I realize it's tough going up against an
institution like Homeland Security. Browsers are now set up to ask first if
you want access, and that seems to me a more reasoned response.
On Fri, Feb 22, 2013 at 2:09 PM, Jennifer L. Muzyka
jennifer.muz...@centre.edu
I've been trying to customized some jmol scripts and I had a couple
questions.
1. Is there an option to change the length of the arrowhead for a 'draw
arrow' or 'draw arrow arc' command?
2. What are the units for the 'scale' parameter for an arc? I've found
that a value of 500 results
Excellent, thanks.
But where is it that I can learn that there such a thing as quaternion()?
--Dan
From: Robert Hanson hans...@stolaf.edu
To: jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.net
Sent: Friday, February 22, 2013 1:47 PM
Subject:
http://chemapps.stolaf.edu/jmol/docs/
On 22 February 2013 23:34, Dan Kirshner dan_kirsh...@yahoo.com wrote:
Excellent, thanks.
But where is it that I can learn that there such a thing as quaternion()?
--Dan
--
*From:* Robert Hanson hans...@stolaf.edu
On Fri, Feb 22, 2013 at 5:23 PM, Spencer Bliven sbli...@ucsd.edu wrote:
I've been trying to customized some jmol scripts and I had a couple
questions.
1. Is there an option to change the length of the arrowhead for a
'draw arrow' or 'draw arrow arc' command?
size overall, but not
http://chemapps.stolaf.edu/jmol/docs/?search=quaternion%28%29#jmolmath
*The quaternion q = quaternion(script(show rotation)) (or, in Jmol 12.2,
just q = quaternion()) measures how much the model has been rotated from
its reference position (with x to the right, y to the top, and z toward the
I'm running Jmol 12.0.22 through BioJava.
We need to get BioJava gurus to move to Jmol 13. (Andreas? Peter?) Maybe
there is a newer version of BioJava than what you are using.
Good point. - I upgraded the BioJava to the latest Jmol version that is
available from Maven central - 13.0.10.
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