Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry‐standard rendering techniques

Rajendiran, Nivedita; Durrant, Jacob D.

doi:10.1002/jcc.25155

Cited by 12 publications

(11 citation statements)

References 39 publications

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“…For example, our BlendMol 20 plugin for the popular 3D modeling program Blender allow users to import VMD- or PyMOL-visualized proteins as meshes. Our Pyrite 25 plugin can then animate these meshes according to MD-captured motions. Additional plugins created by others allow Blender to export animations in file formats that are compatible with JavaScript libraries such as Babylon.js and three.js.…”

Section: Resultsmentioning

confidence: 99%

PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser

Pacheco

Kaminsky

Kochnev

et al. 2019

J. Chem. Inf. Model.

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Molecular dynamics (MD) simulations reveal molecular motions at atomic resolution. Recent advances in high-performance computing now enable microsecond-long simulations capable of sampling a wide range of biologically relevant events. But the disk space required to store an MD trajectory increases with simulation length and system size, complicating collaborative sharing and visualization. To overcome these limitations, we created PCAViz, an open-source toolkit for sharing and visualizing MD trajectories via the web browser. PCAViz includes two components: the PCAViz Compressor, which compresses and saves simulation data; and the PCAViz Interpreter, which decompresses the data in users’ browsers and feeds it to any of several browser-based molecular-visualization libraries (e.g., 3Dmol.js, NGL Viewer, etc.). An easy-to-install WordPress plugin enables “plug-and-play” trajectory visualization. PCAViz will appeal to a broad audience of researchers and educators. The source code is available at , and the WordPress plugin is available via the official WordPress Plugin Directory.

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Section: Resultsmentioning

confidence: 99%

PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser

Pacheco

Kaminsky

Kochnev

et al. 2019

J. Chem. Inf. Model.

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“…S5), video rendering (Supplementary Fig. S6 and Video S2) and molecular-dynamics visualization (Rajendiran and Durrant, 2018) (Supplementary Videos S3 and S4).…”

Section: Discussionmentioning

confidence: 99%

BlendMol: advanced macromolecular visualization in Blender

Durrant¹

2018

Bioinformatics

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Summary Programs such as VMD and PyMOL are excellent tools for analyzing macromolecular structures, but they do not implement many of the advanced rendering techniques common in the film and video-game industries. In contrast, the open-source program Blender is a general-purpose tool for industry-standard rendering/visualization, but its user interface is poorly suited for rigorous scientific analysis. We present BlendMol, a Blender plugin that imports VMD or PyMOL scenes into Blender. BlendMol-generated images are well suited for use in manuscripts, outreach programs, websites and classes. Availability and implementation BlendMol is available free of charge from http://durrantlab.com/blendmol/. It is written in Python. Supplementary information Supplementary data are available at Bioinformatics online.

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“…But we are certainly interested in enabling non-interactive MD-trajectory visualization in future versions of ProteinVR. We have already published two browser-based tools for MD-trajectory playback in a non-VR context [50,51]. Incorporating components of these programs into future versions of ProteinVR could be a productive future direction.…”

Section: Featuresmentioning

confidence: 99%

ProteinVR: Web-based molecular visualization in virtual reality

et al. 2020

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Protein structure determines biological function. Accurately conceptualizing 3D protein/ ligand structures is thus vital to scientific research and education. Virtual reality (VR) enables protein visualization in stereoscopic 3D, but many VR molecular-visualization programs are expensive and challenging to use; work only on specific VR headsets; rely on complicated model-preparation software; and/or require the user to install separate programs or plugins. Here we introduce ProteinVR, a web-based application that works on various VR setups and operating systems. ProteinVR displays molecular structures within 3D environments that give useful biological context and allow users to situate themselves in 3D space. Our web-based implementation is ideal for hypothesis generation and education in research and large-classroom settings. We release ProteinVR under the open-source BSD-3-Clause license.

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Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry‐standard rendering techniques

Cited by 12 publications

References 39 publications

PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser

PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser

BlendMol: advanced macromolecular visualization in Blender

ProteinVR: Web-based molecular visualization in virtual reality

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