[Chimera-users] importing sdf files from PubChem
meng at cgl.ucsf.edu
Sat May 5 08:32:10 PDT 2007
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!).
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 May 5, 2007, at 7:32 AM, Mark Andrake wrote:
> 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
> 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 Andrake, Ph.D.
> Research Associate
> Fox Chase Cancer Center
> 7701 Burholme Ave.
> Philadelphia, PA 19111
> mark.andrake at fccc.edu
> Elaine Meng wrote:Hi Mark,
>> I've attached the test.sdf file mentioned in my previous message.
>> 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
More information about the Chimera-users