LocOccupancy – Local computational methods to improve the interpretability and analysis of cryo-EM maps

LocOccupancy is a computational approach to facilitate map interpretation by providing estimated occupancy for density voxels obtained in reconstructions.

Inputs:

  • Required: 3D reconstruction half maps
    • Recommended running information:
      • Use half maps not full reconstructions
      • Do NOT use post-processed or masked maps
      • Upload using Browser upload not Globus
  • Required: Pixel size
  • Required: Threshold
    • Indicate threshold to use for creating a 3D mask during map enhancement
  • Required: Maximum resolution of the sweeping resolution
    • 2-3X global FSC resolution

Advanced options:

  • Minimum resolution of the sweeping resolution: Recommended to use a value of 10-20 Angstroms
  • Threshold significance in comparison with macromolecule: Recommended to use 0.25
  • Bandwidth of the bandpass filter used in Fourier Space: If global resolution is less than 4A, use 3.5-5; If global resolution is greater than 4A, use 6-8A

Outputs

  • 3D volume with voxel values corresponding to estimated occupancy that can be downloaded from the task output page named “LocOccupancy output”

Reference

S. Kaur, J. Gomez-Blanco, A. Khalifa, S. Adinarayanan, R. Sanchez-Garcia, D. Wrapp, J. S. McLellan, K. H. Bui, J. Vargas, Local computational methods to improve the interpretability and analysis of cryo-EM maps. bioRxiv

Github

Link