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
- Recommended running information:
- 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