[Chimera-users] Question regarding an inorganic compound to display with Chimera
meng at cgl.ucsf.edu
Fri May 26 11:45:55 PDT 2006
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
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:
> 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.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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