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Barbara Reisner, James Madison University
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Joined: 11/17/2007 - 11:01am

Posting attachments that contain structure

We've moved the discussion of posting attachments out of the "Step by Step - How to Contribute a Learning Object to VIPEr" document to a forum because the community uses many different structure visualization programs.  This post contains some general comments.  We haven't figured out the best way to do things yet so any suggestions that you have will be valuable to the entire community.

There are a large number of file formats that can be used to post static structural images.  Choose your favorite but keep in mind that you want it to be easily read by the largest possible number of users.  In other words, don't choose an obscure file type.

In general, when you want to post a manipulatable structure, you'll need to get it ready so that others can use it.  First, make sure that it's in a format that's readable.  CIF files can be read by a number of free viewers out there (we like Mercury (CCDC) for small molecules and CrystalMaker for extended structures).   There is only one problem with the CIF format:  it won't let you specify the view of the structure that the user will see (specific atoms, polyhedral or space filling, number of unit cells).  To specify structural view, you need to turn to another format.  Jmol works well for small molecules because it works in any browser with Java capabilities (and we're working to get VIPEr working as a Jmol server).  If you only want to specify the view and don't need to remove any atoms (other than hydrogen atoms), consider using Mercury and saving your molecule in the MSY format which will preserve a specific view.  (If you have a site license to the CSD, the special version of Mercury that comes with it will let you entirely dictate how you want a user to view the molecule.)   In my opinion, nothing beats CrystalMaker for extended structures.  There is a free demo version available that can be used to visualize structures and investigate simple things like bond angles and lengths.  However, since CrystalMaker is commercial software, it costs money.  While you can use the demo version as a viewer, you need to own a copy of the software to create files that others can view.  We haven't yet figured out how to make extended structures pretty in Jmol, but there is some documentation available.