scholarly journals Development and assessment of CootVR, a virtual reality computer program for model building

2021 ◽  
Vol 77 (1) ◽  
pp. 19-27
Author(s):  
Hamish Todd ◽  
Paul Emsley
Keyword(s):  
Virtual Reality ◽  
Computer Program ◽  
Model Building ◽  
Three Dimensional ◽  
Specific Model ◽  
Three Dimensions ◽  
Biological Macromolecules ◽  
Data Set ◽  
X Ray Crystallography ◽  
Order Of Magnitude

Biological macromolecules have complex three-dimensional shapes that are experimentally examined using X-ray crystallography and electron cryo-microscopy. Interpreting the data that these methods yield involves building 3D atomic models. With almost every data set, some portion of the time put into creating these models must be spent manually modifying the model in order to make it consistent with the data; this is difficult and time-consuming, in part because the data are `blurry' in three dimensions. This paper describes the design and assessment of CootVR (available at http://hamishtodd1.github.io/cvr), a prototype computer program for performing this task in virtual reality, allowing structural biologists to build molecular models into cryo-EM and crystallographic data using their hands. CootVR was timed against Coot for a very specific model-building task, and was found to give an order-of-magnitude speedup for this task. A from-scratch model build using CootVR was also attempted; from this experience it is concluded that currently CootVR does not give a speedup over Coot overall.

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

TABLES, a program to display space-group symmetry information in three dimensions

1987 ◽  
Vol 20 (6) ◽  
pp. 532-535 ◽  
Author(s):  
C. Abad-Zapatero ◽  
T. J. O'Donnell
Keyword(s):  
Computer Graphics ◽  
Computer Program ◽  
Three Dimensional ◽  
Spatial Location ◽  
Three Dimensions ◽  
Group Symmetry ◽  
Space Group ◽  
Interactive Display ◽  
Symmetry Operators ◽  
Group Information

TABLES is a computer program developed to display the crystal symmetry and the spatial location of the different symmetry operators for a given space group using interactive computer graphics. It allows the three-dimensional interactive display of the space-group information contained in International Tables for Crystallography [(1983), Vol. A. Dordrecht: Reidel]. Such a program is useful as a teaching aid in crystallography and is valuable for exploring molecular packing arrangements.

Immersion, interactivity and three-dimensionality: virtual reality documentation of media art installations

2021 ◽  
Author(s):  
Kira A. Brown
Keyword(s):  
Virtual Reality ◽  
Case Studies ◽  
Three Dimensional ◽  
Research Paper ◽  
Sensory Experience ◽  
Three Dimensions ◽  
Media Art ◽  
Essential Information ◽  
Art Installation ◽  
High Level

This research paper explores the possibilities for virtual reality (VR) documentation of media art installations. Based on an analysis of the characteristics of media art, and a survey of current documentation strategies, this paper investigates the viability of three-dimensional documentation. Four cross-disciplinary case studies are presented and analysed to demonstrate that VR documentation provides an immersive and richer reconstruction of a media art installation in three dimensions. In addition, the interactive components can be simulated within the VR environment, offering the possibility for curators and visitors to virtually re-experience the artwork. The case studies show that, although the creation of VR documentation can be costly and time-consuming, and currently requires a high-level of expertise, it can be a useful addition to established documentation strategies by providing essential information about the visual aspects of the artwork, its environment and the user’s multi-sensory experience.

scholarly journals The Resolution in X-ray Crystallography and Single-Particle Cryogenic Electron Microscopy

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 580
Author(s):  
Victor R.A. Dubach ◽  
Albert Guskov
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particle Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Fourier Transform

X-ray crystallography and single-particle analysis cryogenic electron microscopy are essential techniques for uncovering the three-dimensional structures of biological macromolecules. Both techniques rely on the Fourier transform to calculate experimental maps. However, one of the crucial parameters, resolution, is rather broadly defined. Here, the methods to determine the resolution in X-ray crystallography and single-particle analysis are summarized. In X-ray crystallography, it is becoming increasingly more common to include reflections discarded previously by traditionally used standards, allowing for the inclusion of incomplete and anisotropic reflections into the refinement process. In general, the resolution is the smallest lattice spacing given by Bragg’s law for a particular set of X-ray diffraction intensities; however, typically the resolution is truncated by the user during the data processing based on certain parameters and later it is used during refinement. However, at which resolution to perform such a truncation is not always clear and this makes it very confusing for the novices entering the structural biology field. Furthermore, it is argued that the effective resolution should be also reported as it is a more descriptive measure accounting for anisotropy and incompleteness of the data. In single particle cryo-EM, the situation is not much better, as multiple ways exist to determine the resolution, such as Fourier shell correlation, spectral signal-to-noise ratio and the Fourier neighbor correlation. The most widely accepted is the Fourier shell correlation using a threshold of 0.143 to define the resolution (so-called “gold-standard”), although it is still debated whether this is the correct threshold. Besides, the resolution obtained from the Fourier shell correlation is an estimate of varying resolution across the density map. In reality, the interpretability of the map is more important than the numerical value of the resolution.

scholarly journals BigTop: A Three-Dimensional Virtual Reality tool for GWAS Visualization

2019 ◽  
Author(s):  
Samuel T. Westreich ◽  
Maria Nattestad ◽  
Christopher Meyer
Keyword(s):  
Virtual Reality ◽  
Association Studies ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Gene Location ◽  
P Value ◽  
Genome Wide Association Studies ◽  
Two Dimensional ◽  
Three Dimensional Representation ◽  
Manhattan Plot

AbstractBackgroundGenome-wide association studies (GWAS) are typically visualized using a two-dimensional Manhattan plot, displaying chromosomal location of SNPs along the x-axis and the negative log-10 of their p-value on the y-axis. This traditional plot provides a broad overview of the results, but offers little opportunity for interaction or expansion of specific regions, and is unable to show additional dimensions of the dataset.ResultsWe created BigTop, a visualization framework in virtual reality (VR), designed to render a Manhattan plot in three dimensions, wrapping the graph around the user in a simulated cylindrical room. BigTop uses the z-axis to display minor allele frequency of each SNP, allowing for the identification of allelic variants of genes. BigTop also offers additional interactivity, allowing users to select any individual SNP and receive expanded information, including SNP name, exact values, and gene location, if applicable. BigTop is built in JavaScript using the React and A-Frame frameworks, and can be rendered using commercially available VR headsets or in a two-dimensional web browser such as Google Chrome. Data is read into BigTop in JSON format, and can be provided as either JSON or a tab-separated text file.ConclusionsUsing additional dimensions and interactivity options offered through VR, we provide a new, interactive, three-dimensional representation of the traditional Manhattan plot for displaying and exploring GWAS data.

scholarly journals Pengenalan Rumah Adat di Pulau Jawa Sebagai Media Pembelajaran Berbasis VRML

2015 ◽  
Vol 3 (3) ◽  
pp. 354
Author(s):  
Ari Fitriyanto ◽  
Kodrat Iman Satoto ◽  
Kurniawan Teguh Martono
Keyword(s):  
Information Technology ◽  
Virtual Reality ◽  
Programming Language ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Modeling Language ◽  
Virtual Technology ◽  
Virtual Reality Modeling Language ◽  
Modeling Software ◽  
The Media

Indonesia is rich in culture, ethnicity which one example is the traditional houses that exist in each province. Introduce Indonesian traditional house to users by using information technology as a medium of information could be one way to preserve the nation's culture. Limitations of the media information about traditional houses that currently can only be enjoyed through pictures or visit the traditional houses directly make society can not know the traditional houses in Indonesia optimally. Therefore we need a media so that people can know more about traditional houses in Indonesia without the need to visit directly into sites or less information such as 2-dimensional images in the book. Application developed is combination between virtual reality and website. Application built using the waterfall method. The virtual technology is embedded in a website that allows users to access them anytime and anywhere. Aplication was developed using VRML (Virtual Reality Modeling Language) and 3ds Max modeling software, and using the programming language PHP, HTML, CSS, and MySQL database. The browser needs Cortona3D Viewer plug-in for displaying three-dimensional file. The results of making this application is an application that utilizes the VRML technology to display traditional house on the island of Java in three dimensions. The results show that this application runs in accordance with the design functionality that has been made.

scholarly journals Immersion, interactivity and three-dimensionality: virtual reality documentation of media art installations

2021 ◽  
Author(s):  
Kira A. Brown
Keyword(s):  
Virtual Reality ◽  
Case Studies ◽  
Three Dimensional ◽  
Research Paper ◽  
Sensory Experience ◽  
Three Dimensions ◽  
Media Art ◽  
Essential Information ◽  
Art Installation ◽  
High Level

This research paper explores the possibilities for virtual reality (VR) documentation of media art installations. Based on an analysis of the characteristics of media art, and a survey of current documentation strategies, this paper investigates the viability of three-dimensional documentation. Four cross-disciplinary case studies are presented and analysed to demonstrate that VR documentation provides an immersive and richer reconstruction of a media art installation in three dimensions. In addition, the interactive components can be simulated within the VR environment, offering the possibility for curators and visitors to virtually re-experience the artwork. The case studies show that, although the creation of VR documentation can be costly and time-consuming, and currently requires a high-level of expertise, it can be a useful addition to established documentation strategies by providing essential information about the visual aspects of the artwork, its environment and the user’s multi-sensory experience.

Ulrich Wolfgang Arndt. 23 April 1924 — 24 March 2006

2014 ◽  
Vol 60 ◽  
pp. 39-55
Author(s):  
R. A. Crowther ◽  
A. G. W. Leslie
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Direct Methods ◽  
Biological Molecules ◽  
Data Generation ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography ◽  
Whole Process ◽  
Wide Range

Ulrich (Uli) Arndt was a physicist and engineer whose contributions to the development of a wide range of instrumentation for X-ray crystallography played an important part in our ability to solve the atomic structure of large biological molecules. Such detailed information about protein structures has for the past 50 years underpinned the huge advances in the field of molecular biology. His innovations spanned all aspects of data generation and collection, from improvements in X-ray tubes, through novel designs for diffractometers and cameras to film scanners and more direct methods of X-ray detection. When he started in the field, the intensities of individual X-ray reflections were often estimated by eye from films. By the end of his career the whole process of collecting from a crystal a three-dimensional data set, possibly comprising hundreds of thousands of measurements, was fully automated and very rapid.

scholarly journals Electron crystallography: imaging and single-crystal diffraction from powders

2007 ◽  
Vol 64 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Xiaodong Zou ◽  
Sven Hovmöller
Keyword(s):  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction ◽  
Recent Developments

The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.

scholarly journals Whole-pattern fitting technique in serial femtosecond nanocrystallography

IUCrJ ◽  
2016 ◽  
Vol 3 (2) ◽  
pp. 127-138 ◽  
Author(s):  
Ruben A. Dilanian ◽  
Sophie R. Williams ◽  
Andrew V. Martin ◽  
Victor A. Streltsov ◽  
Harry M. Quiney
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Monte Carlo Integration ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography ◽  
Small Crystals ◽  
Crystallite Structure ◽  
Serial Crystallography

Serial femtosecond X-ray crystallography (SFX) has created new opportunities in the field of structural analysis of protein nanocrystals. The intensity and timescale characteristics of the X-ray free-electron laser sources used in SFX experiments necessitate the analysis of a large collection of individual crystals of variable shape and quality to ultimately solve a single, average crystal structure. Ensembles of crystals are commonly encountered in powder diffraction, but serial crystallography is different because each crystal is measured individually and can be orientedviaindexing and merged into a three-dimensional data set, as is done for conventional crystallography data. In this way, serial femtosecond crystallography data lie in between conventional crystallography data and powder diffraction data, sharing features of both. The extremely small sizes of nanocrystals, as well as the possible imperfections of their crystallite structure, significantly affect the diffraction pattern and raise the question of how best to extract accurate structure-factor moduli from serial crystallography data. Here it is demonstrated that whole-pattern fitting techniques established for one-dimensional powder diffraction analysis can be feasibly extended to higher dimensions for the analysis of merged SFX diffraction data. It is shown that for very small crystals, whole-pattern fitting methods are more accurate than Monte Carlo integration methods that are currently used.

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