Subject: Re: CCL:converting an sdf database into a chemfinder database

From: Richard Wood <rlw28)at(cornell.edu>
Date: Tue, 20 Apr 2004 07:01:07 -0600

Hi all

I should note that the file that I am trying to open and convert, 
CANS03.sdf, is a file that I obtained from the NCI database (I don't 
have the url with me, it's at work), and it originally couldn't be 
opened with CACTVS,  until someone at the NCI "fixed" it.  CACTVS now 
reads it, but won't write it out, at least not the whole file.  The part 
that CACTVS does write out, can be read by Chemfinder, however.  CACTVS 
will currently write out the first 37 structures I believe and then not 
write anymore, but only if I write the first 15 and then append the next 
15 and so on.  SO it writes two sets of 15 structures and then 7 of the 
next 15 and then stops.  I'm doing this using the CACTVS browser, btw.

I hope this helps all of those that responded with questions/suggestions.

TIA,
Richard

Richard L. Wood wrote:

>Hi all
>
>I'm wondering if there is anyway to convert an sdf database into something
>that Chemfinder can read easily.
>
>Chemfinder is supposed to be able to import sdf databases, but the file I
>have must not be formatted correctly, because chemfinder can't read it.
>
>Thanks in advance,
>Richard
>
>
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-- 
Richard L. Wood, Ph. D.
Computational Chemist
SynVax, Inc.
N. Logan, UT 84341

---

From: "Igor Filippov [Contr]" <igorf..at..helix.nih.gov>
Date: Tue, 20 Apr 2004 16:14:15 -0400

Richard,

Is it possible that you're talking about NCI database processed by our
group (CADD @ LMC @ NCI-Frederick) ? The website is
http://cactus.nci.nih.gov where you can download public portion of NCI
database (processed). As the whole processing was done in CACTVS
it is hard to imagine that one is not able to read/write the structures
anymore. If you downloaded NCI database somewhere else then it is, of
course, impossible to tell what did you get and what the problem with it
might be.

Regards,

Igor Filippov
Contractor - SAIC-Frederick
Computer Aided Drug Design group
Laboratory of Medicinal Chemistry
National Cancer Institute

On Tue, 20 Apr 2004, Richard Wood wrote:

> and send your message to:  CHEMISTRY..at..ccl.net
>
> Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net
> Jan Labanowski,  jlabanow..at..nd.edu (read about it on CCL Home Page)