We recently added an animate feature the Jmol Virtual Model Kit -
chemagic.com/vmk/. Basically, the feature simply facilitates the capturing of
molfile frames while editing a model in the VMK window. The resulting
multiframe molfile text can be pasted into the VMK Molecular Editor script
field
Otis. Super. I don't think my latest jme reader will have that problem
with planar rings. I have the z coordinate given a bit of noise. Keep
playing with it. Some boats are probably inevitable.
Sent from my iPhone
On Apr 10, 2010, at 8:59 PM, Otis Rothenberger osrot...@chemagic.com
Otis, if you think it would be valuable, we could look into reading the
stereochemistry of bonds and at least shifting a whole branch up or down an
angstrom in the Z coordinate based on that. wouldn't be perfect, but it
might not be that hard, either.
As I started to do this, I realize that the
Hey, check this out:
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
124. JME reader reads stereochemistry and automatically turns 2D to 3D with
addition of H atoms * The JME format is a two-dimensional file format that
is easy to generate
Bob,
Yes!
I don't have Jmol 12.0 downloaded yet, but I'll get it now. Where are
you seeing the stereo bonds. I don't see any stereo information in the
molfile (other than the SMILES in the header) or the jme string. Are you
reading this from the SMILES?
Once I get this set up, Tom will be
Bob,
I have it set up on my home server. I'm only working with small
molecules, but I haven't had a clunker yet.
Wow, I am impressed!
I actually took the stereo bonds off of the JME on the chemagic site. I
need to put them back.
I'm still going to bypass some other misses. For example,
Isn't that fun? I'll set up a little JME reader for that new.htm page next.
It's the JME string. Previous 11.9 versions won't work because I
inadvertently broke the JME reader and never thought to test it because it
seemed, well, so useless before. But now I think it's pretty neat!.
The JME
Bob,
I installed /Jmol 12.0.RC5/ on the chemagic server and set the JME
transfer code in the model kit for the JME string. In playing with the
new set-up, I did not see one error in stereo rendering of non-cyclic
systems. Structures drawn in the JME editor are processed as follows:
1) If
Otis,
This is a very neat application. I hope it can be tweaked to remedy a
few glitches. When I draw trans-dimethylcyclohexane and load the
molecule the chair conformer of the cis-isomer is displayed. Drawing
the cis-isomer loads the same Jmol display. If I use the X button of
the
Bill,
Thanks for the comments. The 2D to 3D translation is an ongoing problem
for us. The JME editor is light weight and it can be embedded directly
in the application, but it passes only 2D information to Jmol. Jmol
tries to sort this out with the UFF minimization. With really simple
On Fri, April 9, 2010 12:16 pm, Otis Rothenberger wrote:
Downside: It's a helper application. Upside: ACD generously makes
ChemSketch a free download for private, student, educational use.
Isn't ChemSketch a MSWindows-only product?
Rich
Otis,
Are you transferring the JME structure as a Smiles string or as a JME
string. The latter has more information in it.
Bill
Otis Rothenberger wrote:
Bill,
Thanks for the comments. The 2D to 3D translation is an ongoing problem
for us. The JME editor is light weight and it can be
Otis, I think a really simple and fast way to generate a structure would be
to allow clicking on H atoms to sprout CH3 (NH2 or OH or Cl, depending upon
the selected atom choice). If possible, clicking should not allow violation
of the octet rule for C, N, or O.
On Fri, Apr 9, 2010 at 12:07 PM,
Rich,
I'm not a Mac user, but ACD has a Web page that discusses use of their
software on Macs:
http://www.acdlabs.com/support/mac.php
My partner in this project, Tom Newton, is a Mac user (and Windows
user). He may know the answer to your question from experience. I'll
copy him with this
Bob,
Yeah, I'm getting that message!
I was the one that kept pushing for an atom addition approach, but
there's no question that you have both control of chain building and
stereochemistry by using the H (univalent atom) replacement approach. I
think I need to hide that click/add feature in
Bill,
I'm passing molfiles from JME. Actually, the SMILES is also passed in
the molfile (Name Position), but its the molfile that's rendered.
The JME string might be worth a try. While the information is still 2D
only, we have found that you can give UFF minimization good starts and
bad
I need to correct my previous post. I was thinking of MarvinSketch, not ACD's
ChemSketch. Sorry.
J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
pb...@saintmarys.edu
ChemSketch is available, or was a year ago, as Java applet and is platform
independent. I also found it to be more accurate in defining stereochemical
features than was JME. But I was using the SMILES approach from both. I
wanted a student to be able to draw a structure which upon
Bill,
Bob's comment is right on the mark. The fastest route to a model of
choice is selecting the best parent and then building by click/replace
of the hydrogen atoms, which are already in reasonable stereo positions.
In this case, the cyclohexane parent already has the appropriate chair
with
Otis,
By all means trust Bob's advice. I was interested in your approach
inasmuch as the Dundee Server nicely converts simple JME structures into
PDB files that yield beautiful Jmol displays, but does so in a stepwise
fashion.
http://davapc1.bioch.dundee.ac.uk/prodrg/index.html
Bill
Hello-
With the inclusion of UFF minimization in Jmol, I decided to revisit an old
project that I started in the early days of Chime - the design of a virtual
molecular model kit that had the feel of an old Prentice Hall student model
kit. During this recent Jmol stage of the project, Bob Hanson
Hi Otis
Quite an impressive piece of work. Congratulations!
In case you want to look into this, my Firefox 3.6 (WinXP) refuses to
show the video at
http://www.che.ilstu.edu/osrothen/web_molecules/video/VMKquickstart.ht
ml
Says I should upgrade my Flash Player, but it is the latest
10.0.45.2.
I agree that this is looking like a very nice tool.
No problems for me in viewing the video (Firefox 3.6.3, Windows Vista
Ultimate SP2).
Brian
On Thu, Apr 08, 2010 at 04:06:16PM +0200, Angel Herráez wrote:
Hi Otis
Quite an impressive piece of work. Congratulations!
In case you want to
Incredible!! What a great use of Jmol
Eran
__
From Otis Rothenberger o...@chemagic.com
Sent Thu 4/8/2010 3:53 PM
To jmol-users@lists.sourceforge.net
Subject [Jmol-users] Jmol Virtual Model Kit
Hello-
With the inclusion of UFF minimization
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