Subject: Re: CCL: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0

From: Egon Willighagen <e.willighagen:at:science.ru.nl>
Date: Wed, 6 Jul 2005 21:35:36 +0200

On Wednesday 6 July 2005 20:28, Andrew D. Fant wrote:
> Good afternoon all, and thanks to everyone who responded to my previous
> questions about openbabel and descriptor code.  I have one other
> question about software that has come up.

The Chemistry Development Kit (http://cdk.sf.net/) can do this and is free to 
download. The involved Java class is ModelBuilder3D [1]. A live demo is 
available from:

http://www.chemistry-development-kit.org/

Just enter a SMILES or upload a molecular file, and a 3D model will be 
displayed using Jmol [2].

Egon

1. 
http://cdk.sf.net/apicvs/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.html
2. http://www.jmol.org/

-- 
e.willighagen:at:science.ru.nl
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen
http://www.cac.science.ru.nl/people/egonw/
GPG: 1024D/D6336BA6

---

From: Miklos Vargyas <mvargyas:at:chemaxon.com>
Date: Wed, 06 Jul 2005 21:28:15 +0200

Hi Andy,

try Marvin! It is available on the internet, just follow the link below:

http://www.chemaxon.hu/marvin/sketch/demo-applet.html

Draw a structure in the sketch window, then select Edit->Clean->3D. Then 
you can either pop up a 3D viewer (View->Open 3D viewer) or save the 3D 
structure in a suitable file (e.g. mol).

In case you need to convert many structures the MolConverter tool comes 
handy as it can batch process your molecules.
You may wish to visit the molconverter page at 
http://www.chemaxon.hu/marvin/doc/user/molconvert.html.

Regards,
Miklos

Andrew D. Fant wrote:

>question about software that has come up.  Can anyone recommend a
>program that can generate 3D structures of any quality of all from 2D
>representations?  I know that Concord and Corina can do this, but I am
>doing this for my own education/edification and would rather not blow
>the rent money on this project.  I'm hoping to take some data I have
>pulled from various publications on my laptop on a train trip and putter
>with it en route, so a web-based tool is less than ideal.  If anyone has
>any suggestions, I would be most appreciative.
>
>Thanks,
>	Andy
>
>
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