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 http://129.43.27.140/ncidb2/ (I usually search by CAS number) and NLM ChemIDPlus http://chem.sis.nlm.nih.gov/chemidplus/ (process is somewhat elaborate... let me know if you want details) Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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

_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users