Re: [Jmol-users] Can Jmol get the molecule in 3D (Was: loading jmolfile from open babel)

[Philip B. <pb...@sa...>]

I have mucked around with this issue, particularly with my medchem  
class.  I have not found a cheap way to deal with it.  In chemdraw or  
a variety of free programs you can easily create smiles strings.   
Spartan on the Mac can import those and present optimized  
structures.  They can then be saved as pdb files for web viewing with  
jmol.   But that requires spartan.   I have tried to convince  
Cambridge that, since they have the code to convert their drawing to  
chem3d and from there to pdb, they ought to just tack that code onto  
the end of chemdraw and allow export of pdb files, particularly since  
they no longer support 3-D on the mac.  But they have not been so  
inclined.

What one needs is a java program that will take smiles to pdb.  That  
requires some sort of optimizer.

Phil



On Feb 13, 2007, at 4:08 PM, Angel Herraez wrote:

> Hi Paul
>
>> So I tried out ChemSketch but it's windoze only.
>
> Yes!  There is some other similar molecule drawing program, I think  
> it's Mac. Anyway, I don't
> know if it also does 3D conversion.
> Are you on Mac or Linux?
>
> Then , there is a web service doing these tricks. I recommended it  
> before to other user and I
> think it solved his conversion, but I would have to dig it out.  
> Guess it's CORINA. Look for it; if
> you don't find it, I will go back through my old messages.
>
>
>
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J. Philip Bays
Professor of Chemistry
Science Hall 158
Saint Mary's College
Notre Dame  IN  46556
(574) 284-4663