Comments on: Enhanced Structure Viewing on ChemSpider using JMol – Plea for 3D Optimizer http://www.chemspider.com/blog/enhanced-structure-viewing-on-chemspider-using-jmol-plea-for-3d-optimizer.html Building Community for Chemists Tue, 14 May 2013 21:50:31 +0000 hourly 1 http://wordpress.org/?v=3.5 By: ChemSpider Blog » Blog Archive » Another Response to Constructive Feedback from Peter Murray-Rust… http://www.chemspider.com/blog/enhanced-structure-viewing-on-chemspider-using-jmol-plea-for-3d-optimizer.html/comment-page-1#comment-3584 ChemSpider Blog » Blog Archive » Another Response to Constructive Feedback from Peter Murray-Rust… Mon, 15 Oct 2007 06:44:55 +0000 http://www.chemspider.com/blog/?p=92#comment-3584 [...] database to those who ask for it. It will be published in PubChem. We USE Open Source components (1,2,3,4). We have not generated any Open Source components yet and our source code is not Open. We [...]

]]> By: ChemSpider Blog » Blog Archive » More Comments About Diazonamide A - other efforts to distinguish WHAT’S REAL? http://www.chemspider.com/blog/enhanced-structure-viewing-on-chemspider-using-jmol-plea-for-3d-optimizer.html/comment-page-1#comment-2775 ChemSpider Blog » Blog Archive » More Comments About Diazonamide A - other efforts to distinguish WHAT’S REAL? Mon, 24 Sep 2007 05:10:47 +0000 http://www.chemspider.com/blog/?p=92#comment-2775 [...] commented on this already on this blog. We have been sourcing a 3D optimizer since PubChem does not provide 3D coordinates. We have one [...]

]]> By: ChemSpider News » Blog Archive » Enhanced Structure Viewing on ChemSpider using JMol http://www.chemspider.com/blog/enhanced-structure-viewing-on-chemspider-using-jmol-plea-for-3d-optimizer.html/comment-page-1#comment-1447 ChemSpider News » Blog Archive » Enhanced Structure Viewing on ChemSpider using JMol Fri, 03 Aug 2007 03:42:43 +0000 http://www.chemspider.com/blog/?p=92#comment-1447 [...] advantage of this excellent piece of software. The new capabilities are described in detail on the ChemSpider blog. Stumble [...]

]]> By: Egon Willighagen http://www.chemspider.com/blog/enhanced-structure-viewing-on-chemspider-using-jmol-plea-for-3d-optimizer.html/comment-page-1#comment-1349 Egon Willighagen Mon, 30 Jul 2007 06:42:55 +0000 http://www.chemspider.com/blog/?p=92#comment-1349 Antony, I just read this email from Christoph on the cdk-user mailing list, and was not aware of that work: “In addition to what Violeta already said, I can say that we are definitely using this forcefield implementation for energy calculation. We currently use it with a genetic algorithm for minimization which finds the correct minimum, meaning that the energy calculation is largely correct. There maybe some problems with bond stretching farer away from the equilibrium, but if you start with a reasonable structure, you should be fine.”

]]> By: Egon Willighagen http://www.chemspider.com/blog/enhanced-structure-viewing-on-chemspider-using-jmol-plea-for-3d-optimizer.html/comment-page-1#comment-1346 Egon Willighagen Mon, 30 Jul 2007 06:17:49 +0000 http://www.chemspider.com/blog/?p=92#comment-1346 I was already wondering about those weird bond lengths :) BTW, JMol is not the applet behind http://www.jmol.org/, that’s Jmol, with a lower case ‘m’; it happened that there was an american who also wrote a 3D viewer applet (I can no longer find it on the internet), who use JMol as name. The applet shown is Jmol, not JMol.

On the force field code in the CDK, I think Violetta has done a good job in implementing the basics in the CDK, but I do not think the whole project really got a user community of the ground. Your feedback on the optimizer is most welcome, and I hereby invite you to submit it to CDK News, see http://www.cdknews.org/.

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