[Chimera-users] SDF file

Hernando J Sosa hernando.sosa at einstein.yu.edu
Thu Jan 22 06:21:30 PST 2015

Thanks Aldo,

I tried Avogrado and  it does do the trick.



From: Aldo Segura [mailto:aldosegura at gmail.com]
Sent: Wednesday, January 21, 2015 2:35 PM
To: Hernando J Sosa
Cc: chimera-users at 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.

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


Chimera-users mailing list
Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>

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<mailto:asegurac at ipn.mx>; aldosegura at gmail.com<mailto:aldosegura at gmail.com>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20150122/61ea1229/attachment.html>

More information about the Chimera-users mailing list