Molmil: a molecular viewer for the PDB and beyond.

Akira R. Kinjo,Haruki Nakamura,Gert-Jan Bekker

doi:10.1186/s13321-016-0155-1

Akira R. Kinjo, Haruki Nakamura + Show 1 more

Open Access

https://doi.org/10.1186/s13321-016-0155-1

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Abstract

We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user’s local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0155-1) contains supplementary material, which is available to authorized users.

Highlights

Molecular viewers are a vital tool for our understanding of protein structures and functions
We have developed a new web based molecular viewer, Molmil, which can take advantage of graphics processing unit (GPU) hardware acceleration using WebGL
Since Molmil requires at least 6 GB of memory to load the structure into memory, the user’s device must be equipped with 8 GB of memory

Summary

Background

Molecular viewers are a vital tool for our understanding of protein structures and functions. We have developed a new web based molecular viewer, Molmil, which can take advantage of GPU hardware acceleration using WebGL It runs on a wide range of platforms such as Windows, Linux, Mac OSX, Android and iOS. For obvious reasons (potential abuse) we have not made this functionality available as a public REST service, but users can obtain this application from Molmil’s Github page which they can run on their own workstation so that their own machine will build the movie Using this tool, Molmil can e.g. be used to produce high quality MP4 videos of molecular simulation trajectories. More information regarding Molmil as well as use-cases and command-line examples can be found at http://github.com/gjbekker/molmil/wiki

Discussion

Conclusions