[Chimera-users] SDF file

Aldo Segura aldosegura at gmail.com
Wed Jan 21 11:34:37 PST 2015

Hi Hernando,

I think Chimera does not deal with sdf files (either 2D or 3D). Chimera
team please correct me if I'm wrong :)
You should try to open your 2D sdf file with Avogadro program and run some
geometry optimizations. Then, save your file in mol2, pdb, etc. and open it
with chimera if that's what you want.



2015-01-21 12:20 GMT-05:00 Hernando J Sosa <hernando.sosa at einstein.yu.edu>:

>   I have an sdf file  with a small ligand molecule in 2D (it looks flat
> when opened in chimera). What would be the best way to  make it 3D (i.e.
> assign/minimize the proper bond angles & distances). Is it possible to do
> it in chimera?
>  Thanks
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Aldo Segura-Cabrera
Research Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
e-mail: Aldo.Segura-Cabrera at cchmc.org <asegurac at ipn.mx>;
aldosegura at gmail.com
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