Upgrade of D plus software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations

被引：5

作者：

Balken, Eytan ^{[1
]}

Ben-Nun, Itai ^{[1
]}

Fellig, Amos ^{[1
]}

Khaykelson, Daniel ^{[2
]}

Raviv, Uri ^{[1
,3
]}

机构：

[1] Hebrew Univ Jerusalem, Inst Chem, Edmond J Safra Campus, IL-9190401 Jerusalem, Israel

[2] Weizmann Inst Sci, Dept Mol Chem & Mat Sci, IL-76100 Rehovot, Israel

[3] Hebrew Univ Jerusalem, Ctr Nanosci & Nanotechnol, Edmond J Safra Campus, Jerusalem, Israel

来源：

JOURNAL OF APPLIED CRYSTALLOGRAPHY | 2023年 / 56卷

基金：

以色列科学基金会;

关键词：

X-ray scattering; fiber diffraction; hierarchical modeling; D plus software; structure factors; polydispersity; orientations; MOLECULAR-FIELDS;

D O I：

10.1107/S1600576723005319

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

This article presents an upgrade of the D+ software [Ginsburg et al. (2019). J. Appl. Cryst. 52, 219-242], expanding its hierarchical solution X-ray scattering modeling capabilities for fiber diffraction and single crystallographic orientations. This upgrade was carried out using the reciprocal grid algorithm [Ginsburg et al. (2016). J. Chem. Inf. Model. 56, 1518-1527], providing D+ its computational strength. Furthermore, the extensive modifications made to the Python API of D+ are described, broadening the X-ray analysis performed with D+ to account for the effects of the instrument-resolution function and polydispersity. In addition, structure-factor and radial-distribution-function modules were added, taking into account the effects of thermal fluctuations and intermolecular interactions. Finally, numerical examples demonstrate the usage and potential of the added features.

引用

页码：1295 / 1303

页数：9

共 37 条

[1]

Als-Nielsen J ..., 2011, Elements of Modern X-ray Physics

[2] Rapidly Forming Early Intermediate Structures Dictate the Pathway of Capsid Assembly [J].

Asor, Roi ;

Schlicksup, Christopher John ;

Zhao, Zhongchao ;

Zlotnick, Adam ;

Raviv, Uri .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2020, 142 (17) :7868-7882

[3] pH stability and disassembly mechanism of wild-type simian virus 40 [J].

Asor, Roi ;

Khaykelson, Daniel ;

Ben-nun-Shaul, Orly ;

Levi-Kalisman, Yael ;

Oppenheim, Ariella ;

Raviv, Uri .

SOFT MATTER, 2020, 16 (11) :2803-2814

[4] Assembly Reactions of Hepatitis B Capsid Protein into Capsid Nanoparticles Follow a Narrow Path through a Complex Reaction Landscape [J].

Asor, Roi ;

Selzer, Lisa ;

Schlicksup, Christopher John ;

Zhao, Zhongchao ;

Zlotnick, Adam ;

Raviv, Uri .

ACS NANO, 2019, 13 (07) :7610-7626

[5] Crystallization, Reentrant Melting, and Resolubilization of Virus Nanoparticles [J].

Asor, Roi ;

Ben-nun-Shaul, Orly ;

Oppenheim, Ariella ;

Raviv, Uri .

ACS NANO, 2017, 11 (10) :9814-9824

[6] ORNSTEIN-ZERNIKE RELATION AND PERCUS-YEVICK APPROXIMATION FOR FLUID MIXTURES [J].

BAXTER, RJ .

JOURNAL OF CHEMICAL PHYSICS, 1970, 52 (09) :4559-+

[7]

Ben-Nun T., 2019, SC 19 P INT C HIGH P

[8] X plus : a comprehensive computationally accelerated structure analysis tool for solution X-ray scattering from supramolecular self-assemblies [J].

Ben-Nun, Tal ;

Ginsburg, Avi ;

Szekely, Pablo ;

Raviv, Uri .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2010, 43 :1522-1531

[9] Js']Jscatter, a program for evaluation and analysis of experimental data [J].

Biehl, Ralf .

PLOS ONE, 2019, 14 (06)

[10] SASfit: a tool for small-angle scattering data analysis using a library of analytical expressions [J].

Bressler, Ingo ;

Kohlbrecher, Joachim ;

Thunemann, Andreas F. .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2015, 48 :1587-1598

← 1 2 3 4 →