[Chimera-users] reading .sd files

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 16 09:50:53 PDT 2014

Hi Fabian,
The ViewDock tool doesn't read SD format, sorry… there is a list of the formats it knows about here:


You could try converting to one of those formats (pdb, mol2, pdbqt, mae …) with some other tool like Babel, or maybe even in Chimera:

I didn't know anything about .sd but some Googling has led me to believe it is the same as SDF or multi-MOL format.  Chimera can read SDF files, but they aren't recognized specifically as docking results; it would just show all the structures at once.  Only filename extensions .sdf and .mol are automatically recognized as SDF (not .sd) so you would have to specify the "MDL MOL/SDF" type directly or change the filename to open it  in Chimera.  Then you could save as a single multimodel PDB file or Mol2 file using the respective choices in the Chimera File menu.

I don't know what program created your .sd file and I haven't tried this process myself, so I don't know how well the resulting PDB or Mol2 file would work with ViewDock.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 14, 2014, at 5:13 AM, Fabian Glaser <fglaser at technion.ac.il> wrote:

> Hi,
> I have tried to read .sd files with docking ligands, without success.
> Is there a way to ready results of docking in .sd format in Chimera?
> Thanks a lot,
> Fabian

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