A user can launch VMD as a local application from within BioCoRE, visualize a molecular system in an interesting way and then save this view back to BioCoRE. These views are also available to other researchers in the same project. If one researcher discovers something interesting, she can publish a molecular view to BioCoRE, and other researchers can see the same view using VMD. This tool is also very useful for individual researchers because BioCoRE can be used as an automatic archive of a molecule viewing session. Entire collections of views can be published in this manner for later retrieval.
From BioCoRE, Bob starts VMD, the Theoretical and Computational Biophysics Group's molecular visualization program. Here, he loads a file of the protein he and Ann are working on from the BioCoRE filesystem. Once he gets the molecule displayed in a representation and orientation that he feels is meaningful, he saves it back to BioCoRE so that others can view it.
The Control Panel notifies Ann that Bob has published a new state, and she opens it. She and Bob discuss the new state in the chat window, and publish a few more states that focus on different views.
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