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MorphOT: Transport-based interpolation between EM maps with UCSF ChimeraX

Arthur Ecoffet, Frédéric Poitevin, View ORCID ProfileKhanh Dao Duc
doi: https://doi.org/10.1101/2020.09.08.286302
Arthur Ecoffet
1Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
2Department of Applied Mathematics, Ecole Polytechnique, Palaiseau, 91120, France
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Frédéric Poitevin
3Department of Data Analytics, LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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Khanh Dao Duc
1Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
4Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
5Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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  • ORCID record for Khanh Dao Duc
  • For correspondence: kdd@math.ubc.ca
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Abstract

Motivation Cryogenic Electron-Microscopy offers the unique potential to capture conformational heterogeneity, by solving multiple 3D classes that co-exist within a single cryo-EM image dataset. To investigate the extent and implications of such heterogeneity, we propose to use an optimal-transport based metric to interpolate barycenters between EM maps and produce morphing trajectories. While standard linear interpolation mostly fails to produce realistic transitions, our method yields continuous trajectories that displace densities to morph one map into the other, instead of blending them.

Implementation Our method is implemented as a plug-in for ChimeraX called MorphOT, which allows the use of both CPU or GPU resources. The code is publicly available on GitHub (https://github.com/kdd-ubc/MorphOT.git), with documentation containing tutorial and datasets.

Contact kdd{at}math.ubc.ca

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/kdd-ubc/MorphOT

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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MorphOT: Transport-based interpolation between EM maps with UCSF ChimeraX
Arthur Ecoffet, Frédéric Poitevin, Khanh Dao Duc
bioRxiv 2020.09.08.286302; doi: https://doi.org/10.1101/2020.09.08.286302
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MorphOT: Transport-based interpolation between EM maps with UCSF ChimeraX
Arthur Ecoffet, Frédéric Poitevin, Khanh Dao Duc
bioRxiv 2020.09.08.286302; doi: https://doi.org/10.1101/2020.09.08.286302

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