PubMed · 2818324
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P D Sly. 1989. Inhaler technique.. https://pubmed.ncbi.nlm.nih.gov/2818324/
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A procedure, called PBR (phase-bias reduction), has been developed to properly refine heavy-atom derivatives and to generate less biased heavy-atom phases when these derivatives contain common heavy-atom sites. Two independent events are obtained by splitting the refinement and phasing calculations into two stages, the first in which one of the derivatives having common sites is used together with the native amplitudes and the second in which both derivatives with common sites are used simultaneously, with one of them being used as the native data set. Improved centroid phases and the corresponding figures of merit are obtained by phase combination. This procedure has been used in the structure determination of the iron-cluster-containing protein -pyruvate-ferredoxin oxidoreductase. When the common heavy-atom sites are properly treated by the PBR procedure, the resulting calculated centroid phases are improved with respect to classical heavy-atom refinement centroid phases where all derivatives are refined together. This leads to improved electron-density distributions, since anomalous difference Fourier maps calculated with the PBR-refined centroid phases and corresponding figures of merit show more clearly the positions of the iron sites.
Shake-and-Bake is a direct-methods procedure which has provided ab initio solutions for protein structures containing as many as 1000 independent non-H atoms. This algorithm extends the range of conventional direct methods by repetitively, unconditionally and automatically alternating reciprocal-space phase refinement with filtering in real space to impose constraints. The application of SnB to protein-sized molecules is significantly affected by the choice made for certain critical parameters, including the number of peaks used for density modification, the choice of phase-refinement method and the number of refinement cycles. The effects of parameter variation have been studied for six protein structures, all of which are solvable by Shake-and-Bake using data at 1.1 A or higher resolution. Solvability in the resolution range 1.2-1.4 A appears to be enhanced by the presence of heavier atoms (S, Cl). Furthermore, it appears that in this range the ratio of refinement cycles and triplet phase invariants to atoms in the structure must be increased. Large structures lacking atoms of any element heavier than oxygen also require non-traditional parameter values.
We recently conducted a study of a subset of the data collected in the NLM/AHCPR Large Scale Vocabulary Test (LSVT). We studied those 11,387 terms in the LSVT data that were narrower in meaning than the UMLS concepts mapped to. We hypothesized that when one term is narrower in meaning than another, the first and second terms are likely to differ primarily by modification. We compared three lexical processing methods of increasing sophistication and measured the ability of each of these methods to correctly identify the modifiers in the data set. The results indicate that when using the most powerful of the methods, 63% of the term pairs were found to differ only by premodification, by postmodification or by both, 31% share some lexical material, and the remaining 6% have no lexical items in common. The implications of the study are discussed.