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OccuPy

  • Description

    a fast and simple python module and program to estimate local scaling of cryo-EM maps, to approximate relative occupancy and/or resolution, and optionally to equalize the map according to occupancy while suppressing solvent amplification.

  • Usage

    To list all executables provided by OccuPy, run: $ sbgrid-list occupy Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install occupy Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    B. O. Forsberg, P. N. M. Shah, and A. Burt. 2023. A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps. bioRxiv 2023.01.18.524529.


    • *Full citation information available through

  • Webinars

    OccuPY

    SBGrid webinars are hosted with partial support from the NIH R25 Continuing Education for Structural Biology Mentors #GM151273, in collaboration with Co-PI Jamaine Davis of Meharry Medical College.

    Topic: OccuPy: A software tool for heterogeneity - and occupancy analysis of cryo-EM reconstructions based on spatial filtering.

    Presenter: Björn Forsberg, Ph.D, Postdoctoral Fellow, Karolinska Institutet

    Host: Pete Meyer
    Recorded on February 13, 2023

    For more information on OccuPy:

    https://sbgrid.org/software/titles/occupy
    https://occupy.readthedocs.io/en/latest
    https://github.com/bforsbe/OccuPy

  • Keywords

    Electron Microscopy

  • Default Versions

    Linux 64:  0.1.13 (1.1 GB)
    OS X INTEL:  0.1.13 (569.8 MB)

  • Other Versions

      Linux 64:

      0.1.11 (1.2 GB) , 0.1.9 (753.8 MB)

    • OS X INTEL:

      0.1.11 (640.6 MB) , 0.1.8 (80.1 MB)

  • Developers

    Björn Forsberg, Pranav Shah, Alister Burt

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