Subject: 3D to 2D coordinate compression

From: "Gerry Lushington" <[email-masked]>
Date: Wed, 13 Mar 2002 09:45:53 -0600

Hi all,

At the risk of sounding retrograde, does anyone know of a good (preferably
simple, UNIX based) program to project 3D coordinates down to reasonable
looking 2D structures?  Obviously a trivial suggestion could be to
arbitrarily wipe out one axis, but as you can imagine that can produce some
pretty awful looking tangles.

                                      - Gerry

Gerald Lushington, Director
Molecular Graphics and Modeling Laboratory
& Cty Asst Professor of Medicinal Chemistry
University of Kansas
1251 Wescoe Hall Rd.
Lawrence KS 66045-7582
------------------------------------------
3021 Malott Hall          Ph. 785-864-1140
[email-masked]        Fax 785-864-5326
http://www.msg.ukans.edu/~msg/mgm.html

---

From: "M. Nicklaus" <[email-masked]>
Date: Wed, 13 Mar 2002 12:24:00 -0500 (Eastern Standard Time)

> pretty awful looking tangles.

CACTVS (see http://www2.chemie.uni-erlangen.de/software/cactvs/) does a
very good job at this.  You can either use the graphical Structure Browser
(csbr), or write a simple script.

Marc

------------------------------------------------------------------------
 Marc C. Nicklaus, Ph.D.                 NIH/NCI at Frederick
 E-mail: [email-masked]               Bldg 376, Rm 207
 Phone:  (301) 846-5903                  376 Boyles Street
 Fax:    (301) 846-6033                  FREDERICK, MD 21702      USA
          Head, Computer-Aided Drug Design MiniCore Facility
     Laboratory of Medicinal Chemistry, Center for Cancer Research,
 National Cancer Institute at Frederick, National Institutes of Health
       http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm
------------------------------------------------------------------------

---

From: Ferenc Csizmadia <[email-masked]>
Date: Wed, 13 Mar 2002 18:45:41 +0100

Hi Gerry,

>pretty awful looking tangles.
Check out the MolConverter module in Marvin Beans. 
(http://www.chemaxon.com/products.html) 
This is the documenation: http://www.chemaxon.com/marvin/doc/molconvert.html
For example, you will need to call it like this to generate a 2D (MDL) 
Molfile:

    molconvert -2:O1 mol your_input_file > your_output_file

It is in Java, so you can run it in Unix (or Windows or Mac)

Best regards,
Ferenc

-- 
Dr. Ferenc Csizmadia
ChemAxon Ltd.
http://www.chemaxon.com