We have recently been releasing a 3D coordinate generator for the CDK, which is
available for testing at http://www.chemistry-development-kit.org.
There, you can draw a 2D structure in JChemPaint and have it converted into a 3D
structure.
It would not be much effort to include it into JChemPaint.
Be aware, however, that it is by no means as sophisticated as CORINA, and may
fail on structures where it cannot find the right ring coordinates (which it
takes from template in an internal database).
Cheers,
Chris
[EMAIL PROTECTED] wrote:
Hi,
I don't think jchempaint can generate 3D coordinates, perhaps the easiest way
to convert them is to use CORINA
(http://www2.ccc.uni-erlangen.de/software/corina/
free_struct.html) which gives free access for 1000 structures. It just requires
a SMILES string as input.
You might also be interested in iBabel for viewing structures
(http://www.macinchem.fsnet.co.uk/applescripts.htm)
Chris
Message Received: Nov 19 2005, 07:30 AM
From: "Aaron Glimme" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED], [email protected]
Cc:
Subject: [Jchempaint-user] (no subject)
I've been using jchempaint for a while to draw structures for my
chemistry tests, now I need to turn some of them in to 3d models and
I'm having some trouble. I've tried saving the file as a MDL MOL file
and CML files and then opening it in Jmol. There are two issues with
this that I haven't been able to figure out.
The first is the bond length seems really large in Jmol I'm having
trouble getting the files to look like a ball and stick model. The
second is the geometry isn't working, the models come out in a 2d
plane, is there some trick or script I need to run to get the
geometry right. I haven't been able to figure it out yet, any help
would be much appreciated.
I'm using the latest versions of all the apps in Mac OS X 1.4.3.
Aaron Glimme
Berkeley High School
-------------------------------------------------------
This SF.Net email is sponsored by the JBoss Inc. Get Certified Today
Register for a JBoss Training Course. Free Certification Exam
for All Training Attendees Through End of 2005. For more info visit:
http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click
_______________________________________________
Jchempaint-user mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jchempaint-user
-------------------------------------------------------
This SF.Net email is sponsored by the JBoss Inc. Get Certified Today
Register for a JBoss Training Course. Free Certification Exam
for All Training Attendees Through End of 2005. For more info visit:
http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Priv. Doz. Dr. Christoph Steinbeck ([EMAIL PROTECTED])
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
-------------------------------------------------------
This SF.Net email is sponsored by the JBoss Inc. Get Certified Today
Register for a JBoss Training Course. Free Certification Exam
for All Training Attendees Through End of 2005. For more info visit:
http://ads.osdn.com/?ad_idv28&alloc_id845&op=click
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
