Monday, February 16, 2009

Viewing 3D Structures at PubChem

PubChem is now providing 3D structures which you can view or download.  PubChem3D generates a single conformer for molecules which are not too large or too flexible.  You can view the results of this on the compound summary pages.  The Compound Summary page shows the structure of the compound with two tabs at the top: you can choose either the customary 2D view, or a 3D image by clicking the appropriate tab.

You also have the option of an interactive view by clicking either the tetrahedral molecule icon
or the image of the 3D molecule.  There are two options for viewing the molecule.

The first is a web-based viewer that opens a new window and generates an animated gif on the fly.  This web-based viewer takes a little getting used to, and strikes me as rather clumsy.  I don't understand why they did not use a java applet such as Jmol instead.  In fact, Rajarshi Guha's Pub3D site does just this.  Enter a PubChem cid and you can see the 3d structure using Jmol.

The second option for viewing the structure in 3D is to download and install the PubChem 3D Viewer. Windows, Linux and Mac versions are available.  The graphics are nice, but it is limited to the file formats used by PubChem: pc3d, asn,  and sdf for multiple molecule files.  You can load more than one molecule at a time by either opening a multi-molecule sdf file or using the Import option.  With more than one molecule loaded you can toggle between a panel-view which displays all the molecules in a table format, or an overlay mode.  Select which molecules to overlay in the Molecules tab in the right-hand panel.

In addition, the right-hand panel has controls for changing the way the molecule(s) are displayed. Oddly there is no Save function.  There might be no particular need to save the molecular data files from the viewer, but they seem to have gone to some trouble to give a lot of graphics display options.  It's too bad that you cannot save images from the PubChem 3D Viewer.

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