Since positional and displacement parameters are correlated, limiting model flexibility (constrained hydrogen positions) seems to make the onset of additional rotational motion more apparent in invariom refinement, whereas free refinement of positions and seems to lead to an over-parameterized model in HAR.
The following sentence was added to the Discussion: "For small particles the accuracy with which such particles may be aligned is the limiting factor, and omitting rotational searches in the movie refinement will probably not have a noticeable effect".
(For small particles the accuracy with which such particles may be aligned is the limiting factor, and omitting rotational searches in the movie refinement will probably not have a noticeable effect).
To achieve more accurate rotational alignment, not only further refinements in navigation technology but also more careful and precise registration will be necessary.
The initial model used in RELION1.4 refinement was a random rotational average of all the extracted sub-volumes (Bharat et al., 2015).
The 58JS3C design was based on the J-type but with refinements addressing the higher rotational speed and relatively short piston stroke.
Finally, even when X-ray diffraction data were collected, solution and refinement of the structures was hampered by rotational disorder of perfluoroalkyl chains and or the PFAF itself.
Protein structures were prepared using the protein preparation wizard of maestro 9.3 [58], following the default protocol which accounts for energy refinement, hydrogen addition, pKa assignment, and side-chain rotational isomer refinement.
In addition, we adapt our refinement protocol also to the case where the rotational search is restricted to only certain axis of rotations, for instance when the search is constrained to rotations around a membrane surface normal when membrane bound complexes are aligned (Section 2.5).
In the stir zone for the sample processed at 325 rpm rotational rate, the microhardness increase is also predominantly due to grain refinement, as coarse Al3Sc precipitates form heterogeneously at grain boundaries with a platelet-like morphology.
For example even when the rotational sampling is performed at only 60° intervals the stochastic iterative refinement process together with the RCS scoring produces on average errors of 3.1°, while the FCS scoring achieves 2.9° error (Table 1).
