[Chimera-users] importing sdf files from PubChem

[Elaine Meng]

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 at 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 at 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 at 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
>>
>>
>>