l - People

Angle calculation
We calculate the angular position of M of a generated structure in pitch-yaw-roll space as
the σy⋅σx⋅σz rotation that would have to be applied to M of the starting structure in
standard orientation, to obtain a structure similar to the generated one. This was done by
first structurally aligning the generated structure with the starting structure by
minimizing the root-mean-square deviation (RMSD) between the S domains of the two
structures. Then the rotation-translation matrix required to move M of the starting
structure to align optimally with M of the generated structure was computed using
VMD’s ”measure fit” command. The rotational part of the rotation-translation matrix
was then compared to the generic σy⋅σx⋅σz rotation matrix and the unknown angles were
solved for algebraically. Note that the generic matrix is arranged according to the
convention of rotating first about z, then x, then y (corresponding to roll, pitch, and yaw,
respectively, Figure 2). This calculation was performed immediately following each
equilibration step above and the computed pitch,yaw, roll angles were recorded. Note
that in the course of the equilibration the angular position of M will change. We refer to
this as drift, and this will be important when we define the aborted conformers below.
No drift occurs, of course, if the equilibration step is left out. In that case the angular
coordinates of the M’s will be arranged in a regular grid.
Re-docking
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