We are testing out a new 3D molecule optimizer on ChemSpider at present. It appears to be more rugged than our previous algorithm and, in our hands at least, has not yet failed to produce a 3D representation. On general small organics it appears to handle the optimization very well and is quite fast. We welcome your feedback if you have time to test. In order to use the optimizer simply go to a record view, lick on Zoom on the Structure tab (see below) and then click on Show 3D as shown in the second image. Since all coordinates are calculated in real time please note that it can take a few seconds from opening the JMol applet to display of the optimized structure (we need to ad a “calculating….” display element when we have time.

Thins look good for us but we have had a couple of reports of failures and are trying to trace whether it is a browser security setting or not. Please let us know if you have any issues. Thanks

Stumble it!

5 Responses to “Testing out a new 3D optimizer on ChemSpider”

  1. Rajarshi Guha says:

    Can you say where the 3D coord geneartor is from?

  2. Antony Williams says:

    Rajarshi, the optimizer is Balloon. Details are here: http://web.abo.fi/~mivainio/balloon/index.php

  3. Egon Willighagen says:

    I’d really love to see the hydrogens too.

  4. Ilmari Krebs says:

    It’s marvelous. Something what I was musing about for a long time is whether it would be possible to have a stereo view on structures, by rendering the molecule from to slightly different perspectives?



  5. Egon Willighagen says:

    Ilmari, right click on the Jmol applet, choose Console, and type ‘stereo on’.

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