Macs in Chemistry

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augmented reality

Visualizing 3D molecular structures using an augmented reality

 

Another workflow has been published "Visualizing 3D molecular structures using an augmented reality app" https://chemrxiv.org/articles/Visualizing3DMolecularStructuresUsinganAugmentedRealityApp/10031888

I've added it to the How to Page.



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ModelAR added to Mobile Science site

 

ModelAR is a powerful 3D modeling tool for students looking to practice organic chemistry. You can explore chemical structures by creating a molecule on the workspace and quickly toggle to pop into AR. This Augmented Reality feature allows you to interact with virtual molecules in real space. ModelAR brings chemistry to life.

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Durrant Lab Software

 

A reader recently pointed out BlendMol part of a suite of software tools developed by the Jacob Durrant Lab.

BlendMol is a Blender plugin that can easily import VMD 'Visualization State' and PyMOL 'Session' files. BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with popular analysis programs (i.e., VMD/PyMOL). Users can import into Blender the very molecular representations they set up in VMD/PyMOL.

This looks like a very interesting open-source project available on GitHub, however looking at the software page https://durrantlab.pitt.edu/durrant-lab-software/ I see there are a number of other interesting packages.

Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.

Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.

PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser. To encourage use, an easy-to-install PCAViz-powered WordPress plugin enables ‘plug-and-play’ trajectory visualization.

Scoria is a Python package for manipulating three dimensional molecular data. Unlike similar packages, Scoria is written in pure Python and so requires no dependencies or installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g., NumPy, SciPy, MDAnalysis), if present, to speed and extend its own functionality.

Looks like a great resource.


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Augmented Reality in Chemistry

 

The use of augmented and virtual reality in chemistry is slowly starting to gain traction. The initial use of virtual reality in drug discovery is well documented but usually confined to highly specialised hardware which has limited it's exposure to a wider audience. However as described by Jonas Boström at the recent Chemistry on Mobile Devices Meeting Virtual reality smartphone apps making chemistry look and feel cool. This project aims to enhance the learning experience for school chemistry lessons by providing virtual reality viewing of molecules using inexpensive Google Cardboard viewers available online.

Virtual reality smartphone apps are making chemistry look and feel cool. This project aims to enhance the learning experience for school chemistry lessons by providing virtual reality viewing of molecules using inexpensive Google Cardboard viewers.

EduChemVR have a number of apps for download to allow users to interact with macromolecules or learn stereochemistry.

The power of the latest generation of smart phones has enabled scientists to also explore augmented reality. Augmented reality is now being used in a number of situations. To enhance publications as demonstrated by Alistair Crow, if you want to know how to do this instructions are available here. Many people have probably used the superb ChemTube3D website created by Nick Greeves at the University of Liverpool which is an invaluable education resource, this is also accessible via a Smartphone app.

ChemTube3D contains interactive 3D animations and structures, with supporting information for some of the most important topics covered during an undergraduate chemistry degree

More recently some of the pages have been enhanced to provide access to virtual reality models, if you would like to develop similar pages there is an AppleScript droplet to batch convert Jmol files into files suitable for AR.

More recently Mark Costner has released MoleculAR: an augmented reality (AR) app to view molecules in 3D.

The images of molecules for use with the MoleculAR augmented reality app are available on GitHub and there is a more detailed explanation here.


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An Applescript droplet to generate Augmented Reality files from JMol

 

Augmented reality is finding new applications in science, in particular the ability to enhance publications or lecture notes, and viewers can set up a free account with Augment to provide easy access.

I was asked recently if it might be possible to generate an AppleScript droplet that you could simply drop a chemical structure file onto to generate the desired files needed for the Augment, and this is an ideal use case for a droplet.

This script uses Jmol to generate the Wavefront .obj and .mtl files which can be used

You read more about the script and download it here.

Nick Greeves has tweeted an example of its use here and a demo page here.

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The use of augmented reality in chemistry

 

A couple more examples of the use of augmented reality to display chemistry

This also looks interesting.
Touching proteins with virtual bare hands

….A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC Vive and the Oculus Rift utilized in this study, are available at reasonable prices….

https://doi.org/10.1007/s10822-018-0123-0


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A short ‘how-to’ on making macromolecular structures viewable in the ‘Augment’ augmented reality app

 

Allister Crow recently posted a brilliant twitter post of a movie showing a crystal structure in augmented reality: https://twitter.com/Allister_Crow/status/933000138552901632 and he posted a simple HowTo. I've taken the original instructions and expanded them to include a few extra options including how to add colours based on a comment by @tomkazimiers.

You can read the detailed instructions here.



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