17. How to solve some problems that you can find during the execution of the modeling workflow

  • command lines involving communication between ChimeraX and Scipion (scipionwrite, scipionss, scipionrs and scipioncombine) do not work:
    As indicated in FAQ, these commands are plugins installed by the scipion-em-chimera setup. Firstly, check the right installation of the plugin just opening and executing the command line:
    help scipionwrite
    If it is installed, a help page will appear. Otherwise, type in the ChimeraX GUI command line:
    devel install /path_to_scipion3_plugins/scipion-em-chimera/chimera/Bundles/scipion
    where path_to_scipion3_plugins is the path to the directory that contains Scipion3 plugins.
    Close the ChimeraX GUI and start the protocol again.
  • Maxit installation

    • Remember: Maxit requires flex and bison. Install them with sudo apt-get