Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):545-559. doi: 10.1107/S2059798318004655. Epub 2018 May 18.
An algorithm for automatic map sharpening is presented that is based on optimization of the detail and connectivity of the sharpened map. The detail in the map is reflected in the surface area of an iso-contour surface that contains a fixed fraction of the volume of the map, where a map with high level of detail has a high surface area. The connectivity of the sharpened map is reflected in the number of connected regions defined by the same iso-contour surfaces, where a map with high connectivity has a small number of connected regions. By combining these two measures in a metric termed the `adjusted surface area', map quality can be evaluated in an automated fashion. This metric was used to choose optimal map-sharpening parameters without reference to a model or other interpretations of the map. Map sharpening by optimization of the adjusted surface area can be carried out for a map as a whole or it can be carried out locally, yielding a locally sharpened map. To evaluate the performance of various approaches, a simple metric based on map-model correlation that can reproduce visual choices of optimally sharpened maps was used. The map-model correlation is calculated using a model with B factors (atomic displacement factors; ADPs) set to zero. This model-based metric was used to evaluate map sharpening and to evaluate map-sharpening approaches, and it was found that optimization of the adjusted surface area can be an effective tool for map sharpening.
提出了一种自动图谱锐化算法，该算法基于优化锐化图谱的细节和连通性。图谱中的细节反映在包含图谱体积固定分数的等轮廓表面的表面积上，其中具有高细节水平的图谱具有高表面积。锐化图谱的连通性反映在由相同等轮廓表面定义的连通区域的数量上，其中具有高连通性的图谱具有较少的连通区域。通过在称为“调整表面积”的度量中结合这两个度量，可以以自动化的方式评估图谱质量。该度量用于在不参考模型或图谱的其他解释的情况下选择最优的图谱锐化参数。可以通过优化调整表面积来整体锐化图谱，也可以局部锐化图谱，从而得到局部锐化的图谱。为了评估各种方法的性能，使用了一种基于图谱-模型相关性的简单度量，该度量可以再现视觉上选择的最佳锐化图谱。使用 B 因子（原子位移因子；ADPs）设置为零的模型计算图谱-模型相关性。该基于模型的度量用于评估图谱锐化和图谱锐化方法，结果发现优化调整表面积可以成为图谱锐化的有效工具。
