Molmil: a molecular viewer for the PDB and beyond

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.

Keywords: Molecular dynamics; Protein structure visualization; WebGL.

Fig. 1

Rendering of 3j3q using Molmil. 3j3q [28] is the largest PDB entry to date (with more than 2.4 million atoms) and can be visualized using Molmil. Left: cartoon rendering with group colouring. Right: rendering of the molecular surface, coloured by electrostatic potential and hydrophobicity generated by eF-site [1]

Fig. 2

Screenshot of Molmil loading the url: http://gjbekker.github.io/molmil/#molmil.loadPDB(‘1crn’). Indicated are the Main menu on the left which can be used to load files, save PNG images, modify settings and play animations if available. The structures menu on the right can be shown by clicking on the indicated button. The context menu which can be displayed by right clicking on any structures, chains or residues/ligands listed within the structures menu. The command line interface which can be shown by clicking on the indicated button