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The morph trajectory was sterically reasonable, i.e. chains were not broken in the attempt
to interpolate motion.
We found that FlexProt’s Maximal[43, 44] RMSD (Root Mean Square Deviation)
parameter had a strong effect on the results. Therefore when FlexProt gave visibly
incorrect results for a given morph, we reran the program, systematically varying this
parameter. If for one of these runs the program’s hinge identification was consistent with
the observed motion observed in the morph movie, the annotation for that morph was
entered into the database. We discarded immediately those morphs that did not exhibit
clear hinge bending motion. Lastly, we removed redundant morphs using nrdb90[22].
Note that the definition of a hinge given in the introduction allows for a hinge of zero
length. FlexProt indeed often returned such hinges. To deal with this, in all cases one
residue on each side of the hinge, was taken to also belong to the hinge. Thus most
hinges are two residues long. At the end of this process, the computer annotated set
contained 273 morphs.
As described, the computer annotation of hinges requires significant human intervention
and the results were often debatable. Many of the hinge annotations differed slightly but
visibly from the boundary between rigid domains, such that the backbone flexions that
could account for the domain motion were not seen in the predicted hinge region. In
other cases hinges were missed, and some annotations appeared where no hinge existed.
The more flagrantly misannotated hinges were removed from the dataset, but making the
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