Macs in Chemistry

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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.


myChEMBL and Docker under MacOSX


Following on from the release of ChEMBL 20 earlier in the year we now see the release of the MyChEMBL virtual machines supporting a CentOS-based image, along with the existing Ubuntu version. What might be of interest to Mac OS X users is are myChEMBL Docker images.

Docker is an open platform for building, shipping and running distributed application. Docker scontainers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, runtime, system tools, system libraries – anything you can install on a server. This guarantees that it will always run the same, regardless of the environment it is running in. Installation under Linux is straightforward and instructions for Mac OS X are provided.

Installation on OS X is more complicated. This is because the standard OS X installation downloads and configures VirtualBox and runs a very lightweight 64-bit Linux with docker installed. Now the problem is, that it won't work in case of myChEMBL. This is because this Virtual Machine has only 20GB of available disk space and our myChEMBL container is 23GB after decompressing. So in order to use it, you first have to resize the volume, which is explained here:

Once done the steps are very simple:

Download the MyChEMBL image from the FTP. Uncompress Load image into docker Run it

Detailed instructions are provided here

After successful completion of the steps above, you can open you browser and go to if you are running docker locally or http://someotherhost/ if you are running docker on some other host. You should then be able to see myChEMBL launchpad page.


VMWare Fusion 5 released

For those who have the need to use different operating systems then the release of VMWare Fusion 5 is a notable milestone. Not only does it support various flavours of Linux and Windows but now you can run OS X Mountain Lion, OS X Mountain Lion Server, OS X Lion and OS X Lion Server in virtual machines.