[Chimera-users] Question regarding an inorganic compound to display with Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri May 26 11:45:55 PDT 2006

Hi Allen,
Where to find structures is not really a Chimera question. As you  
have probably seen, there are a number of repositories or more  
specific sources of structures, some freely accessible, some  
requiring paid subscriptions.  Once you have obtained 3D coordinates  
for some molecule or complex, if it's not in the right format for  
Chimera, you can generally convert it.  One popular format conversion  
tool is this Babel server:


Chimera can read structures in PDB and Mol2 format currently; the  
snapshot release coming soon (in a week or two) will also read CIF  
and mmCIF.

You didn't say what company is showing a 3D representation of the  
compound.  However, even if there is a picture of the 3D coordinates,  
it does not mean that those coordinates are freely available or even  
experimentally determined (i.e. someone at the company might have  
built a model).

I did take a look in Pubchem and ChemIDplus for this complex.  I  
found entries, at least if (which I suspect is true) it is also known  
as tantalum(+5) ethanolate.  However, they just had flat chemist's  
drawings and not 3D coordinates.  It might be in the Cambridge  
Crystallographic Database, but I believe that requires a subscription  
(i.e. is not freely available).  It might be available somewhere  
else, but again, that is not a Chimera issue (and unfortunately not a  
solved issue either).  All that can be done in cases like this is to  
search the web and follow links, or generate your own theoretical model.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 25, 2006, at 11:46 PM, Allen Stock wrote:

> HI,
> I'm interested in viewing the 3D structure for the following  
> inorganic component: Tantalum Pentaethoxide ... also known as TAETO
> The following company gives a 3D representation of the compound.   
> Any idea where I can find a 3D description that can be displayed  
> with Chimera.
> Thanks for your attention and feedback.
> Regards,
> --Allen
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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