“…Web delivery of VR contents is possible through WebVR. Several packages have reported VR capacities such as Molecular Rift [49], ChimeraX [50], UnityMol [25,51], Narupa [52], Nanome [53] and CootVR. WebVR-capable molecular viewers are less widespread, possibly due to the currently limited browser-support for this technology.…”
Section: Emerging Needs For Molecular Visualizationmentioning
confidence: 99%
“…Mol* also supports shareable remote states. To some extent, the collaborative social features may be targeted by current VR approaches, such as [50,53,55], whereas foundations were laid a long time ago [56][57][58][59].…”
Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few ‘Swiss Army knives’ geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.
“…Web delivery of VR contents is possible through WebVR. Several packages have reported VR capacities such as Molecular Rift [49], ChimeraX [50], UnityMol [25,51], Narupa [52], Nanome [53] and CootVR. WebVR-capable molecular viewers are less widespread, possibly due to the currently limited browser-support for this technology.…”
Section: Emerging Needs For Molecular Visualizationmentioning
confidence: 99%
“…Mol* also supports shareable remote states. To some extent, the collaborative social features may be targeted by current VR approaches, such as [50,53,55], whereas foundations were laid a long time ago [56][57][58][59].…”
Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few ‘Swiss Army knives’ geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.
“…It is developed in C++ for the Windows Mixed Reality headset. The commercial program Nanome (Nanome Inc.) [53] , developed in Unity 2017.4.3f and C#, allows molecular manipulation (e.g., in silico mutagenesis) in addition to molecular visualization. It uses VR to visualize, measure, and analyze drug molecules as 3D structural images.…”
Section: Desktop Applicationsmentioning
confidence: 99%
“…Fig 3. Figure 1 Snapshots of VR scenes including protein structures from the influenza virus or SARS-CoV-2, created using BlendMol [47] , [58] (downloaded from https://git.durrantlab.pitt.edu/jdurrant/blendmol/-/tree/1_2/examples/web-files/virtual-reality ) (top) and Nanome [53] , [54] (bottom), respectively; Nanome images are obtained from Alex et al, 2020, under the license CC BY-NC-ND 4.0. Figure 2 Snapshots of VR scenes including protein structures created using VRmol [60] (top) and ProteinVR [62] (bottom).…”
“…Many molecular and protein visualizations in VR exist, e.g. ChimeraX [5], ProteinVR [2], Nanome [8], as well as frameworks for VR [12] and augmented reality (AR) [3]. Yet, none of these offer a visualization of data in reciprocal space.…”
Figure 1: Overview of the immersive analysis of crystallographic diffraction data in reciprocal space. (a) Visualization: Reflections (spheres; size proportional to intensity), unit cell (center; yellow, cyan, magenta), and orthogonal space axis (right; red, green, blue). (b) Reciprocal lattice (green). (c) Orthographic projection to further assist spatial interpretation. (d) Distance measurement. (e) Indexing: Matching a periodic set of diffraction planes to reflections (red: disaligned, green: closely aligned).
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