Time for Attractive Structure Depictions on ChemSpider
Posted by: Antony Williams in ChemSpider Chemistry, How ChemSpider Runs, Quality and ContentCopyright©2008 Antony Williams
It is finally time to rollout more attractive structure depictions. We have needed some more attractive structure depictions for a while but they have become an absolute must have as we rollout the following new capabilities:
1) The ability to make YOUR chemical blog structure searchable (watch this space…). We suggested one path previously…this is BETTER…
2) Structure balloons for using with our document markup tools, both browser-based and Microsoft Word based
We all judge quality of visual aesthetics quickly. We know a good structure when we see one. This is an announcement that we will be rolling out new structures across the site in the next few days. You will see better looking structures showing up across the site – during deposition, during service-based predictions, during searches and, well, everywhere. While not perfect as yet a little more tweaking and the entire database will be supported by the new structure depiction algorithms. As it is you should see some examples now on the database…one shown below. We welcome your feedback!
Stumble it!
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October 13th, 2008 at 12:14 pm
Out of curiosity, are these depictions from ChemWriter?
October 13th, 2008 at 12:35 pm
Rajarshi, all of the structure depiction work was done in-house. It’s not quite perfect as yet and if you browse you’ll find a few issues but they should be knocked out by end of week. What do you think…like what you see?
October 13th, 2008 at 3:24 pm
Yes, they certainly look nice. What algo are you using generate the 2D coordinates?
October 13th, 2008 at 3:53 pm
Generally we don’t have to generate the 2D coordinates because they are already supplied by our depositors. However, in those cases where we do not have the coordinates we are fortunate enough to have access to the OpenEye OEChem toolkit (thanks to the kindness of OpenEye in their support of ChemSpider) and we use OEChem for structure layout. Their structure CLEANing and layout tools are excellent.
October 14th, 2008 at 8:58 am
I’d like to see the NH in this example as HN, with the hydrogen away from the two bonds the nitrogen is involved in (left-aligned instead of right-aligned).
October 14th, 2008 at 11:55 am
Egon thanks for the feedback. We have some bigger issues to resolve right now about stereogenic protons and size of the images then we can consider tweaking issues like this. Keep the feedback coming..we welcome all input!