Hi Mark, You're welcome! I tried getting an SDF directly from PubChem, and that caused the same error you sent, again fixed by cutting and pasting the contents into another SDF file. Cutting/pasting (or otherwise getting rid of bad invisible characters) is the way to go for SDFs from PubChem, at least for now. We may take a look at those files (although I doubt there is a high demand for viewing 2D structures in Chimera!). Best, 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 May 5, 2007, at 7:32 AM, Mark Andrake wrote:

Elaine,

Thanks so much for your fast reply. I can see from the users group that you guys do such a great job in responding to user questions and concerns.

After a quick gaze and trying on my laptop chimera at home - it looks like there must be a hidden character issue. I also had tried MS Word and saved it as a txt file (in case there was some problem in the browser creating the file) but maybe MS Word does not flatten out the file with just ASCI characters.

Next time I will try cutting and pasting through something like WordPad  first.

In any case your test.sdf opened fine in my laptop chimera. Thanks so much - have a great weekend!

Mark

Mark Andrake, Ph.D. Research Associate

Fox Chase Cancer Center ICR428 7701 Burholme Ave. Philadelphia, PA 19111 215-728-3654 mark.andrake@fccc.edu

Elaine Meng wrote:Hi Mark,

...

I've attached the test.sdf file mentioned in my previous message. Best, 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