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”

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