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

[11] THE STRUCTURE OF SYNTHETIC POLYPEPTIDES .1. THE TRANSFORM OF ATOMS ON A HELIX [J].

COCHRAN, W ;

CRICK, FHC ;

VAND, V .

ACTA CRYSTALLOGRAPHICA, 1952, 5 (05) :581-586

[12] Hierarchical Assembly Pathways of Spermine-Induced Tubulin Conical-Spiral Architectures [J].

Dharan, Raviv ;

Shemesh, Asaf ;

Millgram, Abigail ;

Zalk, Ran ;

Frank, Gabriel A. ;

Levi-Kalisman, Yael ;

Ringel, Israel ;

Raviv, Uri .

ACS NANO, 2021, 15 (05) :8836-8847

[13]

Egelstaff P. A., 1992, INTRO LIQUID STATE, P390

[14] D plus : software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures [J].

Ginsburg, Avi ;

Ben-Nun, Tal ;

Asor, Roi ;

Shemesh, Asaf ;

Fink, Lea ;

Tekoah, Roee ;

Levartovsky, Yehonatan ;

Khaykelson, Daniel ;

Dharan, Raviv ;

Fellig, Amos ;

Raviv, Uri .

JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2019, 52 (01) :219-242

[15] Structure of Dynamic, Taxol-Stabilized, and GMPPCP-Stabilized Microtubule [J].

Ginsburg, Avi ;

Shemesh, Asaf ;

Millgrarn, Abigail ;

Dharan, Raviv ;

Levi-Kalisman, Yael ;

Ringel, Israel ;

Raviv, Uri .

JOURNAL OF PHYSICAL CHEMISTRY B, 2017, 121 (36) :8427-8436

[16] Reciprocal Grids: A Hierarchical Algorithm for Computing Solution X-ray Scattering Curves from Supramolecular Complexes at High Resolution [J].

Ginsburg, Avi ;

Ben-Nun, Tal ;

Asor, Roi ;

Shemesh, Asaf ;

Ringel, Israel ;

Raviv, Uri .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2016, 56 (08) :1518-1527

[17]

Hansen J.-P., 2013, Theory of Simple Liquids with Applications to Soft Matter, P1

[18] Array programming with NumPy [J].

Harris, Charles R. ;

Millman, K. Jarrod ;

van der Walt, Stefan J. ;

Gommers, Ralf ;

Virtanen, Pauli ;

Cournapeau, David ;

Wieser, Eric ;

Taylor, Julian ;

Berg, Sebastian ;

Smith, Nathaniel J. ;

Kern, Robert ;

Picus, Matti ;

Hoyer, Stephan ;

van Kerkwijk, Marten H. ;

Brett, Matthew ;

Haldane, Allan ;

del Rio, Jaime Fernandez ;

Wiebe, Mark ;

Peterson, Pearu ;

Gerard-Marchant, Pierre ;

Sheppard, Kevin ;

Reddy, Tyler ;

Weckesser, Warren ;

Abbasi, Hameer ;

Gohlke, Christoph ;

Oliphant, Travis E. .

NATURE, 2020, 585 (7825) :357-362

[19] How sequence defines structure: A crystallographic map of DNA structure and conformation [J].

Hays, FA ;

Teegarden, A ;

Jones, ZJR ;

Harms, M ;

Raup, D ;

Watson, J ;

Cavaliere, E ;

Ho, PS .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (20) :7157-7162

[20] On the determination of molecular fields - II From the equation of state of a gas [J].

Jones, JE .

PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES A-CONTAINING PAPERS OF A MATHEMATICAL AND PHYSICAL CHARACTER, 1924, 106 (738) :463-477

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