Begin forwarded message:
From: "McKenna, Neil J" <[email protected]>
Date: June 4, 2009 8:01:48 PM GMT-04:00
To: <[email protected]>
Subject: RE: [Jmol-users] chemdraw/Jmol noon: Tetrahedral carbons
appear flat
Hi Phil
Thanks for the info. All my posts to the list are being rejected so
would you be so kind as to post the following on my behalf?
--------------------------------------
Thanks for all the responses everyone. I have been referred to an
Open Source option (Avogadro) and as a couple of people have pointed
out I already have a 3D app as part of the ChemDraw package. I can
just open it in either one, it will render in 3D, then I save a new
mol file, works a treat.
---------------------------------------
Many thanks
Neil
From: Philip Bays [mailto:[email protected]]
Sent: Thursday, June 04, 2009 2:54 PM
To: [email protected]
Subject: Re: [Jmol-users] chemdraw/Jmol noon: Tetrahedral carbons
appear flat
If you are using ChemDraw on a PC, you have the accompanying Chem 3D
which will convert your structure to a 3D image. The structure can
also be copied as a smiles string using the edit menu. Will Jmol
read smiles strings? I don't remember.
Phil
On Jun 4, 2009, at 1:22 PM, Angel Herráez wrote:
Hello nmckenna
As far as I know, ChemDraw is a drawing package and, as such, only
does flat (2D) structures. Your problem is not only the carbons, but
the whole molecule.
Apart from searching for corticosterone 3D models in the web, you can
either use a 3D modeling/drawing program (Avogadro comes to my mind)
or use a program or web server that does the 3D optimization starting
from the 2D model.
Several options that I know:
* Avogadro, a 3D editor
* EASIEST: use Jmol to 3D optimize (not always works satisfactorily,
but for simple molecules usually does well; beware that
stereochemistry may be broken during the optimization). Open the 2D
model in a recent version of Jmol (app or applet) and in the pop-up
menu at the top there is "minimize"
* in Windows, ChemSketch Freeware does 2D drawing and 3D
optimization.
* find the Corina web server (a test free service) that will build 3D
models from either a 2D model that you draw online or a SMILES string
* PubChem, among others, has a nice collection of ready-made models,
both 2D and 3D
Lets us know your progress. BTW, your attachment was removed.
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J. Philip Bays
Professor of Chemistry
Science Hall 172
Saint Mary's College
Notre Dame IN 46556
(574) 284-4663
J. Philip Bays
Professor of Chemistry
Science Hall 172
Saint Mary's College
Notre Dame IN 46556
(574) 284-4663
------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
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