Thanks Aldo,
I tried Avogrado and it does do the trick.
Best
Hernando
From: Aldo Segura [mailto:aldosegura@gmail.com]
Sent: Wednesday, January 21, 2015 2:35 PM
To: Hernando J Sosa
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] SDF file
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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