Subject: Re: CCL:2D to 3D structure conversion

From: [email-masked] (Joel Polowin)
Date: Wed, 19 Jul 95 09:48:33 -0400

> Date: Wed, 19 Jul 95 02:18:47 PDT
> From: Scott William Chinn <[email-masked]>
> Subject: CCL:2D to 3D structure conversion
> 
> I understand that programs such as CONCORD, CORINA and CHEM-X
> can convert 2D structures to 3D. 
> 
> I have a number of 2D structures which I would like to 
> convert to 3D and then store in a relational database.
> 
> Is this possible? What does the 3D data look like? I have heard
> that CHEM-X will give you something like 400 bitwise operators, which
> somehow describe the 3D stucture. Is this correct?

Conversion from 2D to 3D is a function offered by several packages
(including ours).  Basically, a set of relatively simple rules is used
to generate 3D geometry, using standard bond lengths and angles.  The big
problem is that the 2D structure is usually quite different from the
desired 3D result; often the 2D structure doesn't have a lot of cues for
stereochemistry or overall conformation.  You should check the results
of such an automated conversion before using them.  (After all, even in
doing a 3D structural optimization by standard methods one sometimes
finds a local minimum that is, by the standards of an intelligent chemist,
obviously a poor structure.  A 2D --> 3D structure conversion is a still
cruder operation.)

I don't know relational databases.  When HyperChem does a 2D --> 3D
conversion, what comes out is a 3D structure: each atom has 3D coordinates
and a set of bonds to other atoms.

Regards,
Joel
 
------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: [email-masked] 

Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: [email-masked]    Support questions to: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]
WWW: http://www.hyper.com/