{"title":"块状溶剂掩膜的通用参数。","authors":"Alexandre Urzhumtsev, Paul Adams, Pavel Afonine","doi":"10.1107/S2053273324000299","DOIUrl":null,"url":null,"abstract":"<p><p>The bulk solvent is a major component of biomacromolecular crystals that contributes significantly to the observed diffraction intensities. Accurate modelling of the bulk solvent has been recognized as important for many crystallographic calculations. Owing to its simplicity and modelling power, the flat (mask-based) bulk-solvent model is used by most modern crystallographic software packages to account for disordered solvent. In this model, the bulk-solvent contribution is defined by a binary mask and a scale (scattering) function. The mask is calculated on a regular grid using the atomic model coordinates and their chemical types. The grid step and two radii, solvent and shrinkage, are the three parameters that govern the mask calculation. They are highly correlated and their choice is a compromise between the computer time needed to calculate the mask and the accuracy of the mask. It is demonstrated here that this choice can be optimized using a unique value of 0.6 Å for the grid step irrespective of the data resolution, and the radii values adjusted correspondingly. The improved values were tested on a large sample of Protein Data Bank entries derived from X-ray diffraction data and are now used in the computational crystallography toolbox (CCTBX) and in Phenix as the default choice.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":null,"pages":null},"PeriodicalIF":1.9000,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913670/pdf/","citationCount":"0","resultStr":"{\"title\":\"Universal parameters of bulk-solvent masks.\",\"authors\":\"Alexandre Urzhumtsev, Paul Adams, Pavel Afonine\",\"doi\":\"10.1107/S2053273324000299\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The bulk solvent is a major component of biomacromolecular crystals that contributes significantly to the observed diffraction intensities. Accurate modelling of the bulk solvent has been recognized as important for many crystallographic calculations. Owing to its simplicity and modelling power, the flat (mask-based) bulk-solvent model is used by most modern crystallographic software packages to account for disordered solvent. In this model, the bulk-solvent contribution is defined by a binary mask and a scale (scattering) function. The mask is calculated on a regular grid using the atomic model coordinates and their chemical types. The grid step and two radii, solvent and shrinkage, are the three parameters that govern the mask calculation. They are highly correlated and their choice is a compromise between the computer time needed to calculate the mask and the accuracy of the mask. It is demonstrated here that this choice can be optimized using a unique value of 0.6 Å for the grid step irrespective of the data resolution, and the radii values adjusted correspondingly. The improved values were tested on a large sample of Protein Data Bank entries derived from X-ray diffraction data and are now used in the computational crystallography toolbox (CCTBX) and in Phenix as the default choice.</p>\",\"PeriodicalId\":106,\"journal\":{\"name\":\"Acta Crystallographica Section A: Foundations and Advances\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.9000,\"publicationDate\":\"2024-03-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913670/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Acta Crystallographica Section A: Foundations and Advances\",\"FirstCategoryId\":\"1\",\"ListUrlMain\":\"https://doi.org/10.1107/S2053273324000299\",\"RegionNum\":4,\"RegionCategory\":\"材料科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/2/9 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q3\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Acta Crystallographica Section A: Foundations and Advances","FirstCategoryId":"1","ListUrlMain":"https://doi.org/10.1107/S2053273324000299","RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/2/9 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
摘要
体溶剂是生物大分子晶体的主要成分，对观察到的衍射强度有很大影响。精确的大体积溶剂建模被认为对许多晶体学计算非常重要。由于其简单性和建模能力，大多数现代晶体学软件包都使用平面（基于掩膜）大体积溶剂模型来计算无序溶剂。在该模型中，体溶剂的贡献由二元掩膜和尺度（散射）函数定义。掩膜在规则网格上使用原子模型坐标及其化学类型进行计算。网格步长和两个半径（溶剂和收缩）是控制掩膜计算的三个参数。这三个参数高度相关，它们的选择是计算掩膜所需的计算机时间和掩膜精度之间的折衷。本文证明，无论数据分辨率如何，都可以使用 0.6 Å 的唯一网格步长值对这一选择进行优化，并相应调整半径值。改进后的值已在从 X 射线衍射数据中提取的大量蛋白质数据库条目样本上进行了测试，现在已作为默认选择用于计算晶体学工具箱（CCTBX）和 Phenix 中。
The bulk solvent is a major component of biomacromolecular crystals that contributes significantly to the observed diffraction intensities. Accurate modelling of the bulk solvent has been recognized as important for many crystallographic calculations. Owing to its simplicity and modelling power, the flat (mask-based) bulk-solvent model is used by most modern crystallographic software packages to account for disordered solvent. In this model, the bulk-solvent contribution is defined by a binary mask and a scale (scattering) function. The mask is calculated on a regular grid using the atomic model coordinates and their chemical types. The grid step and two radii, solvent and shrinkage, are the three parameters that govern the mask calculation. They are highly correlated and their choice is a compromise between the computer time needed to calculate the mask and the accuracy of the mask. It is demonstrated here that this choice can be optimized using a unique value of 0.6 Å for the grid step irrespective of the data resolution, and the radii values adjusted correspondingly. The improved values were tested on a large sample of Protein Data Bank entries derived from X-ray diffraction data and are now used in the computational crystallography toolbox (CCTBX) and in Phenix as the default choice.
期刊介绍：
Acta Crystallographica Section A: Foundations and Advances publishes articles reporting advances in the theory and practice of all areas of crystallography in the broadest sense. As well as traditional crystallography, this includes nanocrystals, metacrystals, amorphous materials, quasicrystals, synchrotron and XFEL studies, coherent scattering, diffraction imaging, time-resolved studies and the structure of strain and defects in materials.
The journal has two parts, a rapid-publication Advances section and the traditional Foundations section. Articles for the Advances section are of particularly high value and impact. They receive expedited treatment and may be highlighted by an accompanying scientific commentary article and a press release. Further details are given in the November 2013 Editorial.
The central themes of the journal are, on the one hand, experimental and theoretical studies of the properties and arrangements of atoms, ions and molecules in condensed matter, periodic, quasiperiodic or amorphous, ideal or real, and, on the other, the theoretical and experimental aspects of the various methods to determine these properties and arrangements.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
