Certain empirical cases published at StrucClues ( http://strucclue.ornl.gov)
identify pairs of tertiary substructures A and B, where it is intuitively
obvious that A is a more compact version of B.
Not a smaller version of B, in the sense that A lacks a helix or strand that
is present in B.
But rather, a more compact version of B, in the sense that A has less
residues per helix, and/or less residues per strand, and/or less residues per
turn.
Since such pairs of tertiary substructures were identified using a novel
methodology (SCILD) that does not depend on any degree of primary structure
sequence homology between substructures A and B, it is impossible to do a
principled structural alignment of A and B using gap insertions because there
is no principled reason for putting the gaps one place rather than another.
(See StrucClues site for explication of the SCILD methodology.)
So
under the assumption that StrucClues cases of this type actually do
reflect some real or valid aspect of tertiary structure, it would seem that
the only way to align substructure A with
substructure B would be by scaling up A or scaling down B. By scaling
up, I mean artificially
increasing the distiance between any two residues r(i) and r(i+1) of A, without
changing the orientation of r(i) with respect to r(i+1). (And vice-versa, for
scaling down.)
How easy would it be to add such a scaling capability to JMol displays?
Assuming again, of course, that it is empirically defensible to do such scaling
(based on the kinds of cases accumulating at StrucClues)?
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