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Supported Applications

calc_level_chimeraX

  • Description

    is a ChimeraX plugin to predict and visualize isosurface levels for 3D density maps. This tool is based on a 3D-CNN initially developed to predict the isosurface levels of 3D density maps, as required by SIREn. More details about the 3D-CNN and SIREn can be found here.

  • Usage

    To list all executables provided by calc_level_chimeraX, run: $ sbgrid-list calc_level_chimerax Copy to clipboard

  • Usage Notes

    For using calc_level plugin in ChimeraX in SBGrid: 1. Open ChimeraX 2. In the ChimeraX command line type "open /programs/x86_64-linux/calc_level_chimerax/1.0.0/bin/calc_level.py" 3. Usage: Open a volume in ChimeraX and in the ChimeraX command line type: "volume calc_level #1"

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install calc_level_chimerax Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    L. F. Kinman, M. V. Carreira, B. M. Powell, and &. J. H. Davis. 2025. Automated model-free analysis of cryo-EM volume ensembles with SIREn. Cell Press Journal. Structure. 33(5): 974-987.


    • *Full citation information available through

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