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.

Errors

If your job crashes due to the 3D volume exceeding job memory limits, there will not be any output 3D volume on the output page. Instead, you will see that the ‘Scheduler standard error’ file has the following text:

/cm/local/apps/slurm/var/spool/job2128600/slurm_script: line 26: 98973 Killed matlab -nodisplay -nosplash -nodesktop -r "run('runLocSpiral.m');exit" > stdout.txt 2> stderr.txt
slurmstepd: error: Detected 1 oom-kill event(s) in step 2128600.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.

Resubmit the job by checking the box next to the advanced option “Advanced: Check box if your job is crashing because of memory issues” to increase the memory allocated to this job.

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