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.

Best,

Aldo

2015-01-21 12:20 GMT-05:00 Hernando J Sosa <hernando.sosa@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@cchmc.org; aldosegura@gmail.com
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