Local B-factor estimation – Local computational methods to improve the interpretability and analysis of cryo-EM maps

Local B-factor estimation is a computational approach to facilitate map interpretation. For this tool, the output reconstruction assigns voxel-by-voxel local B-factor values.

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: Resolution
    • Indicate global FSC resolution value

Advanced options:

  • 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 6-8)
  • Low resolution limit: Recommended to use a value of 15-10 Angstroms
  • Number of sampling points: Recommended value of 10.
  • Threshold for noise significance comparison: Recommended to use 0.95

Outputs

  • 3D reconstruction that provides voxel-by-voxel local B-factor estimates to be displayed by mapping it onto a 3D reconstruction.

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