考虑溶剂不均匀性：镶嵌模型。
Accounting for nonuniformity of bulk-solvent: A mosaic model.
机构信息
Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Bioengineering, University of California Berkeley, Berkeley, California, USA.
出版信息
Protein Sci. 2024 Mar;33(3):e4909. doi: 10.1002/pro.4909.
A flat mask-based model is almost universally used in macromolecular crystallography to account for disordered (bulk) solvent. This model assumes any voxel of the crystal unit cell that is not occupied by the atomic model is occupied by the solvent. The properties of this solvent are assumed to be exactly the same across the whole volume of the unit cell. While this is a reasonable approximation in practice, there are a number of scenarios where this model becomes suboptimal. In this work, we enumerate several of these scenarios and describe a new generalized approach to modeling the bulk-solvent which we refer to as mosaic bulk-solvent model. The mosaic bulk-solvent model allows nonuniform features of the solvent in the crystal to be accounted for in a computationally efficient way. It is implemented in the computational crystallography toolbox and the Phenix software.
基于平面掩模的模型几乎普遍用于大分子晶体学中，以解释无序（整体）溶剂。该模型假设晶体单元中任何未被原子模型占据的体素都被溶剂占据。假定整个单元体积内的溶剂具有完全相同的性质。虽然这在实践中是一个合理的近似，但在许多情况下，该模型变得不够理想。在这项工作中，我们列举了其中的几种情况，并描述了一种新的建模整体溶剂的通用方法，我们称之为镶嵌整体溶剂模型。镶嵌整体溶剂模型允许以计算效率的方式考虑晶体中溶剂的非均匀特征。它在计算晶体学工具箱和 Phenix 软件中实现。
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