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 <asegurac@ipn.mx>; aldosegura@gmail.com =========================================

Hi Hernando, Chimera does read SDF files, but only 3D SDF files will be useful. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#molstruct> 2D SDF files are used for when people just want to display the chemical diagrams. In my opinion, you can’t really convert these into 3D by minimization in Chimera because the atom types won’t be recognized correctly in the first place, just from the flat diagram. You would need to obtain a 3D SDF of the molecule instead. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 21, 2015, at 9:20 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:

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