Molstack: A platform for interactive presentations of electron density and cryo-EM maps and their interpretations

Protein Sci. 2020 Jan;29(1):120-127. doi: 10.1002/pro.3747. Epub 2019 Oct 25.


In the Special Issue on Tools for Protein Science in 2018, we presented Molstack: a concept of a cloud-based platform for sharing electron density maps and their interpretations. Molstack is a web platform that allows the interactive visualization of density maps through the simultaneous presentation of multiple datasets and models in a way that allows for easy pairwise comparison. We anticipated that the users of this conceptually simple platform would find many different uses for their projects, and we were not mistaken. We have observed researchers use Molstack to present experimental evidence for their models in the form of electron density maps, omit maps, and anomalous difference density maps. Users also employed Molstack to present alternative interpretations of densities, including rerefinements and speculative interpretations. While we anticipated these types of projects to be the main use cases, we were pleased to see Molstack used to display superpositions of different models, as a tool for story-driven presentations, and for collaboration as well. Here, we present developments in the platform that were driven by user feedback, highlight several cases that used Molstack to enhance the publication, and discuss possible directions for the platform.

Keywords: cryo-EM; crystallography; data interpretation; validation; visualization.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cloud Computing
  • Computational Biology / methods*
  • Cryoelectron Microscopy
  • Models, Molecular
  • Protein Conformation
  • Proteins / chemistry*
  • Software
  • User-Computer Interface


  • Proteins