A number of ChemSpider users have asked us to provide enhanced viewing of chemical structures and suggested that we use the JMol Open Source viewer. THis is an excellent example of a piece of Open Source software that has continued to advance in capabilities year on year with dozens of websites now taking advantage of this excellent piece of software. An example image is shown below for Bilirubin. In order to see any of the structures from ChemSpider displayed in JMol simply click on Jmol shown in the bottom right hand side of the structure image in the results set.

Bilirubin

























A set of expanded menus are available using a simple right hand click to display a long list of choices for alternative viewing options and other operations. Documentation is available online.Expanded Menus




UNFORTUNATELY, if you rotate the displayed structures you will see that the structures are “flat”. All structures in ChemSpider are presently stored as 2D structures. We would like to offer our users the ability to view and download optimized 3D structures…so we are presently investigating the potential application of the CDK and the possibility to use the force field optimizer available in the developers kit. Watch this space.

Stumble it!

5 Responses to “Enhanced Structure Viewing on ChemSpider using JMol – Plea for 3D Optimizer”

  1. Egon Willighagen says:

    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/.

  2. Egon Willighagen says:

    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.”

  3. ChemSpider News » Blog Archive » Enhanced Structure Viewing on ChemSpider using JMol says:

    [...] advantage of this excellent piece of software. The new capabilities are described in detail on the ChemSpider blog. Stumble [...]

  4. ChemSpider Blog » Blog Archive » More Comments About Diazonamide A - other efforts to distinguish WHAT’S REAL? says:

    [...] commented on this already on this blog. We have been sourcing a 3D optimizer since PubChem does not provide 3D coordinates. We have one [...]

  5. ChemSpider Blog » Blog Archive » Another Response to Constructive Feedback from Peter Murray-Rust… says:

    [...] 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 [...]

Leave a Reply