Monte Carlo-based rigid body modelling of large protein complexes against small angle scattering data

Meesters, Christian; Pairet, Bruno; Rabenhorst, Anja; Decker, Heinz; Jaenicke, Elmar

doi:10.1016/j.compbiolchem.2010.05.002

Cited by 2 publications

(3 citation statements)

References 36 publications

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“…The fit of the present model to the experimental data can be evaluated with a mouse click. Computational refinement of a model is possible in the current version of the software by means of a Monte Carlo procedure, which is a commonly chosen method for this type of refinement (Meesters et al, 2010).…”

Section: Resultsmentioning

confidence: 99%

“…SITUS, for example, recommends the molecular graphics program VMD (Humphrey et al, 1996) for this purpose (http://situs.biomachina.org/tutorial_saxs.html). Similarly, SAS_RIGID (Meesters et al, 2010) is centred around Monte Carlo computations, outsourcing the scattering intensity evaluation to CRYSOL or CRYSON (Svergun et al, 1998). The program MASSHA offers model visualization and manipulation, but also has a built-in feature to compute the scattering intensity of the model (Konarev et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

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Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

Hofmann

Whitten

2014

J Appl Cryst

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Small-angle X-ray scattering has established itself as a common technique in structural biology research. Here, two novel Java applications to aid modelling of three-dimensional macromolecular structures based on small-angle scattering data are described. MolScat is an application that computes small-angle scattering intensities from user-provided three-dimensional models. The program can fit the theoretical scattering intensities to experimental X-ray scattering data. SAFIR is a program for interactive rigid-body modelling into low-resolution shapes restored from small-angle scattering data. The program has been designed with an emphasis on ease of use and intuitive handling. An embedded version of MolScat is used to enable quick evaluation of the fit between the model and experimental scattering data. SAFIR also provides options to refine macromolecular complexes with optional user-specified restraints against scattering data by means of a Monte Carlo approach.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

Hofmann

Whitten

2014

J Appl Cryst

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“…SciPy (Virtanen et al, 2020), NumPy (van der Walt et al, 2011), Matplotlib (Hunter, 2007) and LMFIT (Newville et al, 2014). Many packages to evaluate SAXS data have been programmed in Python (Meesters et al, 2010;Kriegner et al, 2013;Knudsen et al, 2013;Kieffer & Karkoulis, 2013;Evrard et al, 2011;Benecke et al, 2014;Ashiotis et al, 2015;Taché et al, 2013). Since Python is an increasingly popular tool in the SAXS community, it was also chosen for ipyChord.…”

Section: Introductionmentioning

confidence: 99%

ipyChord: a package for evaluating small-angle X-ray scattering data of fiber symmetry

Li¹

2021

J Appl Cryst

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This article presents a Python-based package, ipyChord, to compute the 2D chord distribution function (CDF) from the small-angle X-ray scattering (SAXS) pattern from polymer materials with fiber-symmetrical nanostructure. The program allows construction of a harmonized SAXS pattern from a raw SAXS pattern, by normalization of the incident-beam intensity, absorption correction for sample thickness, masking blind areas on the detector, and filling in the shadow of the beamstop and its holder using symmetry operations. Patterns from modular detectors with inter-module gaps can still be fully constructed satisfactorily after determining the optimized beam position and a radial basis function. A CDF pattern computed from the full SAXS pattern can be used to determine the domain size and its variability using a graphical method. An interface distribution function computed from Bonart's longitudinal projection or sliced from a CDF meridian can quantify differently stacked hard and soft domains. Two cases of the application of ipyChord are presented. The software is open source and available at https://github.com/isaxs/ipyChord.

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Monte Carlo-based rigid body modelling of large protein complexes against small angle scattering data

Cited by 2 publications

References 36 publications

Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

ipyChord: a package for evaluating small-angle X-ray scattering data of fiber symmetry

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