[Chimera-users] SDF format

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 12 10:26:42 PST 2006

Hi Randy,
This is somewhat tangential to your main question, but I believe the  
SDF files from PubChem only contain 2D coordinates, i.e. flat  
"chemist's diagrams" ... probably not what you really wanted.  This  
conclusion is based on a limited sample of structures I've  
investigated personally, so it is possible that there are also SDFs  
with 3D coordinates in there.  If you click SDF Display for a PubChem  
entry, you can see whether the third coordinate column is all zeroes  
or not.

For finding 3D coordinates of small molecules, sites I've found  
useful in the past are

the NCI database browser
(I usually search by CAS number)

and NLM ChemIDPlus
(process is somewhat elaborate... let me know if you want details)

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 12, 2006, at 5:57 AM, Randy Heiland wrote:

> Just wanted to ask about Chimera's support for reading in SDF  
> formatted
> files, e.g. from PubChem.  It seems not to be one of the supported  
> formats.
> Obviously we can use a converter to get pdb format, but thought I'd  
> ask the
> experts.
> Thanks, Randy
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