OASIS4.0—a new version of the program OASIS for phasing protein diffraction data

<正>The program OASIS4.0 has been released.Apart from the improved single-wavelength anomalous diffraction (SAD) phasing algorithm described in a separate paper,an important new feature in this version is the automation of the iterative phasing and model-building process in solving protein structures.A new graphical user's interface(GUI) is provided for controlling and real-time monitoring the dual-space iterative process.The GUI is discussed in detail in the present paper.     

低级晶系Patterson法多解的一般形式(Ⅱ)——多解型相角关系式

为了使用直接法处理Patterson法的多解问题,引入了一个与重原子赝对称性相关的“赝结构”模型,并由此导出了多解型相角关系式。文中指出多解型相角关系式与超结构型相角关系式、结构振幅分量关系式的关系,并以单斜晶系所属的七个非中心对称空间群为例,在轻原子具有双解时,给出了多解型相角关系式的简化形式。 关键词：     

Solving a superstructure from two-wavelength x-ray powder diffraction data － a simulation

Two different kinds of phase ambiguities are intrinsic in two-wavelength x-ray powder diffraction from acentric crystal structures having pseudo-translation symmetry. In a test calculation we have solved the problem for the first time by two different phasing procedures developed originally in single-crystal structure analysis. They are the direct method of breaking enantiomorphous phase ambiguity in protein crystallography and that of breaking translational phase ambiguity for superstructures. An artificial structure was used in the test, which is based on atomic coordinates of the known structure, SHAS (C_5H_6O_5N_3K), with the atom K replaced by Rb. The arrangement of Rb atoms possesses a subperiodicity of t=(a+b+c)/2. Two-wavelength synchrotron x-ray powder diffraction data were simulated with λ_1=0.0816nm and λ_2=0.1319nm. Overlapped reflections were uniformly decomposed at the beginning and redecomposed afterward when the partial-structure information became available. The enantiomorphous phase ambiguity was resolved only for reflections with h+k+l even. Phases of reflections with h+k+l odd were derived by the direct method of solving superstructures. A fragment was then obtained, which led to the complete structure in five cycles of Fourier iteration.     

Ab-initio determination of the incommensurate modulated structure of Bi-2212 from x-ray powder diffraction data －a simulation

A set of x-ray powder diffraction data of the high-T_c superconductor Bi_2Sr_2Ca_1Cu_2O_y (Bi-2212) was simulated based on the experimental single-crystal diffraction data by merging together reflections with diffraction angles (2θ) closer to each other than 0.04 degrees. There are three types of overlapping in the powder diffraction data, i.e. (i) overlapping of main reflections; (ii) overlapping of satellite reflections and (iii) overlapping of main and satellite reflections. The third type of overlapping was first separated into main and satellite components according to the ratio between the average intensity of that of types (i) and (ii). Then the overlapped reflections of main reflections and those of the satellites were uniformly partitioned. Heavy-atom sites in the basic/average structure were found using the uniformly decomposed main reflections by the conventional direct method. Phases of the satellites were derived by the multidimensional direct method. The resultant four-dimensional Fourier maps revealed correctly the essential feature of the modulation. No assumption on either the basic structure or the modulation is needed.     

用直接法提高抗生蛋白链菌素电子显微像的分辨率

将直接法相位外推运用于抗生蛋白链菌素的二维电子衍射数据，相位外推所需的结构因子振幅和初始相位分别来自电子衍射数据和相应的电子显微像。利用最大熵原理识别法和团簇分析方法从多重解中推导出最佳解，最终使电子显微像的分辨率由3 ?提高到2.5 ?，图像质量得到显著改善。     

Patterson图的电子计算机分析

本文提供一个用电子计算机自动分析Patterson图的方案,介绍了据此设计的程序,并通过几个典型的例子说明它的实际应用。 关键词：     

同步辐射在固体物理研究中的应用

一、引 言 二十年前,人们对固体中的电子态就已经有较深的了解,但是只限于金属材料的费米能级附近的电子态和半导体材料中价带顶与导带底附近的电子态,其原因在于:与这些电子态相联系的光学跃迁过程所涉及到的光学频段是红外光、可见光和紫外光,而这些频段的光源制作与探测技术又比较成熟.随着对固体光学性质研究的深入,要获得固体中价带深处和原子的核心能级的资料,就必须扩展到真空紫外频段。在这个频段上,经典的放电管发出的真空紫外光强度较弱,并且阴极溅射造成很厉害的污染,制作工艺也较复杂,所以这种光源显然不够好。电子同步加速器发…     

求解非中心对称晶体结构的人工相位退化法(Ⅱ)——试解P21空间群含重原子的复杂晶体结构

本文用一个比较复杂的、含重原子的晶体结构试验了人工相位退化法,获得了满意的结果。 关键词：     

求解非中心对称晶体结构的人工相位退化法

在用直接法推引非中心对称晶体结构因子的相位时,如果人为地使相位退化为实分量的正负号,可以获得同时包含真实结构及其对映体的E图。利用分量关系式不难使这样的E图复原,从而解出结构。这样做,对于每一个参加相位排列的起始衍射只需考虑两种可能的相位值(0或π),因而比通常的相位排列法节省计算量。 关键词：     

直接法中相位退化问题的处理

相位退化是直接法应用中的一大问题。所谓相位退化,系指非中心对称晶体结构因子的相位在推引或修正过程中收敛为中心对称类型的相位,属于P2₁、P4₁等空间群的晶体,常会出现这一情况。相位退化使相应的E图添加了一个对称中心,这使E图中“鬼峰”的数目大增,因而往往导致直接法的失败。本文提出一种两步处理方法:先将晶体当作中心对称求解以获得一个同时包含真正结构及其对映体的、中心对称的赝结构;然后在此基础上利用所谓分量关系式从赝结构解出真正的结构。此法经用已知结构的晶体检验,证明效果良好。