Re: CCL:2D chemical structure generation

 >I have a molecule (several molecules actually) in an SD formatted file.
 >The connectivity and stereochemistry are correct, but the coordinates
 >are bogus.  Is there a program out there that can generate reasonable
 >looking 2-D coordinates (preferably in SD format) for the compounds?
 ChemOffice Ultra for Windows will do this.  We ran the public NCI SD file
 (127,000 compounds with connectivity but no coordinates) overnight.  No
 particular problems, except for some highly-bridged polycycles which aren't
 going to look particularly good in two dimensions without lots of subjective
 human attention.
 >Alternatively, is there a program that can convert a set of SMILES
 >strings in a file to reasonable looking 2-D structures in SD format
 >(with the proper stereochemistry)?
 ChemOffice Ultra will do this as well.
 Jonathan Brecher
 CambridgeSoft Corporation
 jsb[ AT ]camsoft.com