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extra breakpoints based on visual inspection of the structure, but we were reluctant to
introduce possible experimentor bias. Based on the outcome of the evaluations presented
here, and on the observed distribution of actual hinge points in the larger set of TLSMD
breakpoints, we hope to be able to automate such filtering in the future. To a significant
extent, however, this filtering is done by HingeMaster. The StoneHinge, hNMa, hNMd,
and FO1 predictors, which have many predictions and low specificity, tend to “select” the
TLSMD breakpoints corresponding to domain hinge motion, while “deselecting” those
corresponding to fragment hinges or other motions.
We found that some of the hinges predicted by TLSMD were close to HAG hinges with
high frequency. The remaining TLSMD predictions often correctly reflected motions of
fragments smaller than domains, and these tended not to coincide with the predictions of
other methods. An additional stage of either manual or automated curation of the
TLSMD results would remove most of these fairly easily. In particular, TLSMD would
benefit greatly from an improved ability to combine multiple chain segments from the
initial analysis to yield a description of ‘domains’ in the usual sense. The MurA analysis
in the supplements provides a good example of this. The essential features of the
structure are captured well by the TLSMD partition into 6 continuous chain segments.
The close three-dimensional proximity of the boundaries at residues 20/21 and 228/229
are easily interpreted as belonging to a single inter-domain hinge; the further subdivision
of the obvious continuous domain into 3 chain segments is easily interpreted as the
presence of a small flexible loop (residues 108-127) protruding from a larger continuous
domain. The C-terminal tail of ~20 residues is also flexible, but is not relevant to the
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