Measuring lattices

被引:1
作者
Andrews, Lawrence C. [1 ]
Bernstein, Herbert J. [2 ]
机构
[1] Ronin Inst, 9515 NE 137th St, Kirkland, WA 98034 USA
[2] Ronin Inst, Brookhaven Natl Lab, NSLS II, Upton, NY 11973 USA
来源
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES | 2023年 / 79卷
基金
美国国家卫生研究院;
关键词
Delaunay; Delone; Selling; lattices; unit cell; KRAIT BUNGARUS-CAERULEUS; CRYSTAL-STRUCTURE; NIGGLI REDUCTION; PHOSPHOLIPASE A(2); REDUCED CELLS; IDENTIFICATION; RESOLUTION; SEQUENCE; GEOMETRY; SPACE;
D O I
10.1107/S2053273323004692
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Unit cells are used to represent crystallographic lattices. Calculations measuring the differences between unit cells are used to provide metrics for measuring meaningful distances between three-dimensional crystallographic lattices. This is a surprisingly complex and computationally demanding problem. A review is presented of the current best practice using Delaunay-reduced unit cells in the six-dimensional real space of Selling scalar cells S-6 and the equivalent three-dimensional complex space C-3. The process is a simplified version of the process needed when working with the more complex six-dimensional real space of Niggli-reduced unit cells G(6). Obtaining a distance begins with identification of the fundamental region in the space, continues with conversion to primitive cells and reduction, analysis of distances to the boundaries of the fundamental unit, and is completed by a comparison of direct paths with boundary-interrupted paths, looking for a path of minimal length.
引用
收藏
页码:485 / 498
页数:14
相关论文
共 47 条
  • [1] SOME REMARKS ON REDUCED CELLS
    ALLMANN, R
    [J]. ZEITSCHRIFT FUR KRISTALLOGRAPHIE KRISTALLGEOMETRIE KRISTALLPHYSIK KRISTALLCHEMIE, 1968, 126 (04): : 272 - &
  • [2] Andrews L., 2001, C/C++ Users Journal, V19, P40
  • [3] Andrews L, 2022, ACTA CRYSTALLOGR A, V78, pA81
  • [4] Generating random unit cells
    Andrews, Lawrence C.
    Bernstein, Herbert J.
    [J]. JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2022, 55 : 782 - 786
  • [5] A space for lattice representation and clustering
    Andrews, Lawrence C.
    Bernstein, Herbert J.
    Sauter, Nicholas K.
    [J]. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2019, 75 : 593 - 599
  • [6] Selling reduction versus Niggli reduction for crystallographic lattices
    Andrews, Lawrence C.
    Bernstein, Herbert J.
    Sauter, Nicholas K.
    [J]. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2019, 75 : 115 - 120
  • [7] NearTree, a data structure and a software toolkit for the nearest-neighbor problem
    Andrews, Lawrence C.
    Bernstein, Herbert J.
    [J]. JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2016, 49 : 756 - 761
  • [8] The geometry of Niggli reduction: BGAOL - embedding Niggli reduction and analysis of boundaries
    Andrews, Lawrence C.
    Bernstein, Herbert J.
    [J]. JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2014, 47 : 346 - 359
  • [9] Authier A, 2013, IUCR T CRYS, P1, DOI 10.1093/acprof:oso/9780199659845.001.0001
  • [10] The Protein Data Bank
    Berman, HM
    Westbrook, J
    Feng, Z
    Gilliland, G
    Bhat, TN
    Weissig, H
    Shindyalov, IN
    Bourne, PE
    [J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 235 - 242