I finally had a chance to read Angel's book on Jmol. I learned a lot, and now
I'm wondering when volume 2 might be available.
-Jennifer
Jennifer Muzyka
Professor of Chemistry
On sabbatical at University of Kentucky College of Pharmacy
Centre College
Danville, KY 40422
[EMAIL
I just showed some of the capabilities of Jmol in group meeting for the group
where I'm doing my sabbatical. There was a lot of interest in the features of
Jmol, so I have a couple of questions. The first one is whether it would be
possible for Jmol to calculate and display volumes of the
Bob-
You're right that that I'm having a lot of fun learning about proteins and
ligands and calculations involving their interactions on my sabbatical. I'm at
the University of Kentucky College of Pharmacy working with Chang-Guo Zhan, a
physical chemist. The group does structure based drug
I just tried the demo on the jmol.sourceforge.net page, and I get a an error
instead of the demo. The error says: java:security.AccessControlException.
-Jennifer
Jennifer Muzyka
Professor of Chemistry
On sabbatical at University of Kentucky College of Pharmacy
Centre College
Danville, KY
Angel-
Thanks for the additional information about the protein cavities / isosurfaces.
I tried following your advice about clearing my Java cache in order to get the
Jmol applet on the front page to work, but my browser keeps getting a Page Load
Error for the jmol wiki. I was having the same
Tom-
THANKS for the suggestion about stripping out the port number on the wiki URL.
I did that and the page loaded in a jiffy!
-Jennifer
Message: 5
Date: Wed, 1 Oct 2008 10:58:10 -0700
From: Thomas Stout [EMAIL PROTECTED]
Subject: Re: [Jmol-users] jmol demo on sourceforge
To:
I had no trouble watching the Jmol movie on my computer, running Windows XP.
-Jennifer
Message: 2
Date: Wed, 1 Oct 2008 12:25:34 -0500
From: Robert Hanson [EMAIL PROTECTED]
Subject: [Jmol-users] jmol movie
To: jmol-users@lists.sourceforge.net
Message-ID:
[EMAIL PROTECTED]
I've used Chem3D and Spartan to make movies. I liked Chem3D better because
Spartan would sometimes change the xyz coordinates to yzx when I changed from
one structure to the next.
-Jennifer
--
Message: 1
Date: Mon, 8 Dec
that they don't become invisible. I
don't see any settings that I can tweak to increase the dot density in the
documentation, however. I would appreciate any advice or suggestions anybody
has to keep the dots from disappearing. Thanks!
Jennifer
Jennifer L. Muzyka
Professor of Chemistry
Centre
It works on my iPad! Amazes me - very cool!
Jennifer
Jennifer Muzyka
Professor of Chemistry
Centre College
Danville, KY. 40422
jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
Message: 2
Date: Thu, 12 Apr 2012 17:39:19 -0500
From: Robert Hanson hans...@stolaf.edu
Subject: Re:
efforts!
Jennifer
Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY 40422
jennifer.muz...@centre.edu
http://web.centre.edu/muzyka/
--
Everyone hates slow websites. So
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
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.edumailto:jennifer.muz...@centre.edu wrote:
Does anybody know about a JSmol version of WebMO? We're going to have
trouble doing computational chemistry
Evans
Department of Chemistry
University of Illinois, Urbana-Champaign
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 WebMO? We're going to have
trouble doing computational chemistry experiments in our
This is excellent, many thanks for starting this work. You might want
to touch bases
with Henry Rzepa (Imperial) who I think does read this list. He had a
project a while
back to do something similar. A quick question the data files have the
extension .bak
is this correct? I thought jcamp were
Bob-
We haven't conquered integration yet, so we appreciate the tip!
-Jennifer
-Original Message-
Message: 2
Date: Mon, 02 May 2005 12:54:14 -0500
From: Bob Hanson [EMAIL PROTECTED]
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] RE: Jmol-users digest, Vol 1 #667 - 2
I'm finally trying to start converting some of my chime tutorials to jmol, and
I'm having a tough time getting a very simple example to work. I basically
copied the simple example in the demonstration pages. I've tried several
approaches, all of them unsuccessful. I tried running the page
Miguel-
The file (http://web.centre.edu/muzyka/organic/butane/butane.xyz) DOES exist.
Simple.htm and butane.xyz ARE in the same directory (with the same spelling and
the same case).
Angel's suggestion allowed me to get something working, although I didn't have
exactly the same situation as he
I get the exact same response, even after uploading a new copy of the file to
the directory. Clearly there's a problem with either my ftp program or
something.
The explanations about the relative positions of the relevant files helps too.
I was definitely making some mistakes there. Thanks
I've been working with students building a java applet to display jcamp
data. You can see the project in its current state at
http://jchemapplet.sourceforge.net/. There's still a fair amount of
work to do--tweaking the decompression algorithms to get them just
right, adding axes, adding
AS A USER, WHAT DO YOU WANT?
a) Do you implement callbacks? If so, which ones?
I implement the animFrameCallback to help coordinate other JavaScript
things I like to show simultaneously with some animations.
b) What WOULD you use if you had it available?
I can't think of other callbacks that I'd
that will describe how I control
the options that hide or show the box that allows me to query databases? That
unnecessary option is likely to confuse users of my app. Thanks.
Jennifer
Jennifer L. Muzyka
Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY 40422
jennifer.muz
I am trying to figure out why we have no trouble with current files in the in
the Spectral Zoo (http://chemserv.centre.edu/listing3.php?cat=nmr) but we
cannot see “archived files” that are nested in a folder. I suspect it has to
do with the file paths. The error we see says
When my students are using IE on their spectra, they are unable to modify their
integrals. The problem happens on multiple computers. I think all computers
were running Win7. These problems are observed at
http://chemserv.centre.edu/listing3.php?cat=nmr
I tell the students to use a different
Is it possible to display an isosurface from a function (xy or xyz) in JSmol?
When I try to do this with scripts from Jmol example pages, it crashes
JavaScript. Those example pages might be from old versions of Jmol (11 or 12).
So maybe this capability is no longer supported?
Jennifer
Thanks to Eric and Otis and others who have offered suggestions. I am coming
to believe that something is indeed wrong with my installation. Yesterday I
downloaded the zip file from Sourceforge. Then I copied the jsmol folder to
the server. When I try to open the example files
We recently got a new server to host the SpectralZoo
(http://chemserv.centre.edu/muzyka/spectralzoo), with new versions of PHP and
MySQL. Some of my SpectralZoo scripts broke, so I thought it might be time to
upgrade the Jmol (actually JSmol) that I’m using on the site. I see even more
ic.org/>
On Jun 13, 2016, at 9:11 AM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
Thanks for Angel and Otis for helping me with the troubleshooting. After I
cleared my cache, it works for me too! I’m embarrassed to make such
Thanks for Angel and Otis for helping me with the troubleshooting. After I
cleared my cache, it works for me too! I’m embarrassed to make such a silly
mistake.
Jennifer
Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
ol/specZoo.php
Is this the page that you were referencing in your latest note?
Otis
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jun 13, 2016, at 9:11 AM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz.
It is working for me. It was a cache problem, like Angel and you both
suggested.
Jennifer
Jennifer Muzyka
H. W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
Danville, KY 40422
jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
InChI is very messy because there’s more than one version of the program that
generates it. So depending on what version you use, you get a different InChI.
That information about which version of the InChI rules you are using is an
early part of the string. The other problem with InChI is
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
On Fri, Jul 22, 2016 at 8:42 AM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
InChI is very messy because there’s more than one version of the program that
generates it. So dep
g
859-238-5413
fax 859-236-7925
On Jul 22, 2016, at 10:10 AM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
On Fri, Jul 22, 2016 at 8:42 AM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
InChI is v
Thanks for this encryption code, Otis!
All along I've been skeptical about issues comparing strings, especially since
I would get them from JSME. Now I figured out how to get JSME to spit out
SMILES with slashes for E/Z stereochem. And I see that comparing those strings
is a big problem. Even
I’m not sure if this listserv is the proper place for me to ask this question,
but I’m not sure where else to ask. I’m using the JSME embedded within
Jmol/JSmol to let students practice reaction questions where they can draw
products. The ability to draw starting materials is currently in
correct the fact that \ in a character escape in
JavaScript.
Otis
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org
On Jul 18, 2016, at 3:39 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
I
ication. How hard would it be to return the correct SMILES on each of
these GETS?
Otis
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org
On Jul 19, 2016, at 4:35 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.e
where appropriate? Are
they all JSME SMILES? Is there a possibility that the database creators may
have drawn explicit hydrogens on carbon in non-stereo contect?
Otis
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 19, 2016,
other items or
keys are in the database?
Otis
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 19, 2016, at 4:01 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
Oti
thenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org
On Jul 19, 2016, at 8:22 PM, Jennifer L. Muzyka
<jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>> wrote:
Otis,
What you are describing is essentially how I handle the code for the page wh
abase entirely from Resolver (maybe
PubChem) by an automated process would be a great real world project for one of
the student teams. ( cc to Bob B)
Otis
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org<http://chemagic.org/>
On Jul 19, 2016, at 8:
approach) you will also have to
make some options selections in JSME, but you will also be able to use E/Z and
stereochemistry.
How large is your SMILES database?
--
Otis Rothenberger
o...@chemagic.org<mailto:o...@chemagic.org>
http://chemagic.org
On Jul 19, 2016, at 1:23 PM, Jennifer L. M
Bob,
I was under the impression that canonical SMILES would be the same from one
program to another, not just from the same program. I participated in the Fall
2015 OLCC on cheminformatics, and that’s what I remember us teaching the
students. So the distinction you are making is reasonable to
iSpartan has something like that built into their app rather than calculating
things on the fly. I’m not aware of any other database that has the
information you’re looking for, Bob.
Jennifer
Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600
iSpartan doesn't do any calculations. It looks up data somewhere and only works
for the 50k included molecules. I'm not sure if all the data is included in the
app or maybe it looks up stuff online.
I am not familiar with the file formats Spartan is using these days.
Jennifer
Sent from my
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