[Jmol-users] MarvinSketch

[Robert B. G. <rob...@uk...>]

>Message: 1
>Date: Tue, 29 Jun 2004 17:11:15 +0200 (CEST)
>From: "Miguel" <mi...@jm...>
>To: jmo...@li...
>Subject: [Jmol-users] MarvinSketch?
>Reply-To: jmo...@li...
>
>Glenn & Robert wrote:
>>>Hi, does anyone know of a plug-in for j-mol that enables you to build
>>>molecules and manipulate the atom positions before exporting as xyz files
>>>for calculations? If not does anyone plan to write one?
>>
>>  If you are an academic, you can freely use MarvinSketch to draw the
>>  molecule, minimize it, and export it in a variety of formats.  See
>>  http://www.chemaxon.com/test/marvin/doc/dev/example-sketch1.1.html .
>
>I am not familiar with MarvinSketch ... but I think that many of these
>applets only generate 2D coordinates. When rendered in Jmol the results
>may not be acceptable.

Actually, that is only half true.  When you draw the structure, it is 
indeed drawn in 2D, but you can then minimize the structure in 3D to 
generate the 3D coordinates.  (Choose Edit -> Clean -> 3D -> Clean in 
3D.)  You can also generate a series of conformers of the compound 
and import the 3D coordinates of one conformer back into the 2D 
viewer.  (Choose Edit -> Clean -> 3D -> Select conformers.)  The 
structure can be exported in any number of formats.  It's a really 
powerful applet.  Try it and see. 
http://www.chemaxon.com/marvin/demos.html

I concur with the comments on ChemDraw and Chem3D.  Asking 
Cambridgesoft to add a feature is like asking God to help you win the 
lottery.  It might happen sooner or later, but probably not, and even 
if it does, your request probably had very little to do with it.

-- Bob