[Chimera-users] SDF file

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 21 12:49:32 PST 2015

Hi Hernando,
Chimera does read SDF files, but only 3D SDF files will be useful.

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.

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 at 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

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