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首页> 外文期刊>Acta crystallographica. Section D, Structural biology. >Polder maps: improving OMIT maps by excluding bulk solvent
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Polder maps: improving OMIT maps by excluding bulk solvent

机译：除去大部分低地地图:改善省略地图溶剂

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摘要

The crystallographic maps that are routinely used during the structure‐solution workflow are almost always model‐biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk‐solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit‐cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk‐solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. The tools described in this manuscript have been implemented and are available in PHENIX .
机译：经常使用的晶体地图在工作流几乎结构检测解决方案总模型的偏见,因为模型信息用于计算。也用于验证原子模型由于模型建立和细化,这构成一个紧迫的问题:任何补充道模型将在地图和体现从而阻碍验证。通用工具来验证中原子的存在该模型。地图是排除问题的原子结构,更新相应的结构因素和计算剩余地图。预计,如果这些原子中晶体结构的电子密度省略了原子将被视为积极的功能在这张地图。这几乎是平的散装量溶剂模型广泛用于现代晶体细化项目。在任何的体元恒电子密度单位细胞体积不占领原子模型。因省略了原子是弱大部分溶剂模型可能进一步模糊。这个问题可能的解决方案是预防大部分溶剂进入选中的省略地区,这可能提高解释剩余的地图。波尔德(省略)地图。特别有用的显示弱的密度配体、溶剂分子侧链,替代构象和残留终端区域和循环。这手稿中描述实现,在凤凰是可用的。

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