Quality of alignment

The quality of alignment in the oriented membrane samples was examined by P-NMR. Figure 4A shows that the lipids are well oriented at all temperatures above and below the lipid phase transition at Tm 23 °C. Any potential disturbance of the bilayer by the peptide was also examined by P-NMR, using a very high peptide lipid ratio of 1 10 in multilamellar vesicles. The charac-... 

Figure 3 An example of the quality of alignment. The L3 spectrum (solid line) was aligned on the L2 spectrum (dashed line), using minimization of the square of the difference between the two spectra. The example is for the freshly reduced Pt/K-Al203 catalyst.

Sadreyev, R. I., and N. V. Grishin. 2004. Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinformatics 20 818-28. 

The remaining deviations determine the quality of the alignment (Marzahn, K. 1964) Therefore it is useful for example to define the quality of alignment as follows ... 

It is well known from the early work on surface alignment of liquid crystals [5] that glass surface covered with N,N — dimethyl — N — octadecyl — 3 — aminopropyltrimethoxysilyl chloride DMOAP) orients liquid crystal molecules perpendicularly to the glass surface. The quality of alignment is ex-... 

Polymers which have been subjected to an external field, whether stress, flow, electric or magnetic, may show a preferred alignment of structural units either about, or normal to, the applied field direction. The quality of alignment achieved is generally not perfect in relation... 

Once the molecules are aligned, a molecular field is computed on a grid of points in space around the molecule. This field must provide a description of how each molecule will tend to bind in the active site. Field descriptors typically consist of a sum of one or more spatial properties, such as steric factors, van der Waals parameters, or the electrostatic potential. The choice of grid points will also affect the quality of the final results. 

WR Taylor. Multiple sequence threading An analysis of alignment quality and stability. J Mol Biol 269 902-943, 1997. 

The particular colors that are observed at different angles will depend critically on the thickness of the thin film coating. Precision instrumentation is required to carefully control film thickness during production. The magnitude of the optical effect depends on the density of flakes in the ink, while the quality of the optical effect depends on the precise orientation or alignment of these flakes with respect to the paper surface. 

The contribution of spectrometer surface scatter depends upon the design, quality, and alignment of the spectometer components. Surface scatter may originate from the grating, slits, mirrors, refractor plates, photomultiplier(s), light baffles, interference filters, dust, and the spectrometer interior surfaces. Essentially all internal surfaces may contribute to scatter. 

The good agreement between the folded and the experimental structure is also evident from Figure (l)(center), which shows the secondary structure alignment of the native and the folded conformations. The good physical alignment of the helices illustrates the importance of hydrophobic contacts to correctly fold this protein. An independent measure to assess the quality of these contacts is to compare the C -C distances (which correspond to the NOE constraints of the NMR experiments that determine tertiary structure) in the folded structure to those of the native structure. We found that 66 % (80 %) of the C/3-C/3 distance distances agree to within one (1.5) standard deviations of the experimental resolution. 

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