#28 PubChem XML file

[Heinz Hemken]

There is a new database of small molecules at NCBI
called PubChem:

http://pubchem.ncbi.nlm.nih.gov/

Search for a molecule, select one of the entries that
come back, and scroll down the resulting Substance
Summary page (it has a large 2D structure on the left).
There is a dropdown labeled "Display" and the default
selection is "Summary." You can choose asn1, xml, and
sdf formats for the 3D coordinate file.

So far, so good, right? Choose the SDF format, which
OpenBabel can easily deal with, and you will discover
that the z coordinate is always zero. The structures
are flat on the x,y plane. The asn1 and xml formats
appear to have the complete 3D coordinates (?), but not
in an easily cut-and-pastable format. Their XML format
appears to be home-brewed, but then I am no expert on
file formats.

I wrote to them mentioning the problem.

Heinz

[Geoff Hutchison]

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I'm not sure if the PubChem XML format actually has 3D coordinates --
many that I examined seem to only have 2D coords defined.

But thanks to Chris Morley, the PubChem XML format should now be
supported in OB 2.0.

-Geoff

[SourceForge Robot]

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