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protein in the Jmol window to his/her liking. A GIF image based on that view can be
generated by clicking on the “color by domain” link. The animation will be rendered
using VMD’s “new cartoon” style, with the identified hinge region and two rigid
domains each colored distinctively. The hinge annotations made in this way persist in
our database for visualization and use by others, until overwritten. With minor
modification, these tools were used to generate the Hinge Atlas dataset of manually
annotated hinges. The criteria we used for selection are described in the following
section.
Highlighting the Hinge Atlas hinges (described below) on the animated morph movie is a
matter of going to the morph page and clicking on the “Hinge Analysis” tab as above and
clicking the “Show Hinge Atlas hinge” button. The annotated hinge location will be
rendered in green spacefill style, which contrasts with the white trace used elsewhere in
the protein.
Construction of the Hinge Atlas
The tools described above answer only the technical question of how we annotated
hinges. In this section we clarify the motivation for the Hinge Atlas and its applications
and answer the scientific question of how we decided on the precise location of the hinge
for each morph.
For each morph in the Hinge Atlas, we used the Hinge Annotation Tool as described to
select the hinge location. Motivated in part by our long term goal of providing a resource
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