LocScale is a reference-based local amplitude scaling tool using prior model information to improve contrast of cryo-EM density maps. It can be helpful in the common case of resolution variation in the 3D reconstruction and it can be used as an alternative to other commonly applied map sharpening methods.

References:

• Jakobi AJ, Wilmanns M, Sachse C. Model-based local density sharpening of cryo-EM maps. Elife. 2017 Oct 23;6.

• LocScale Main Site
• LocScale GitHub Project

• Module Name: LocScale (see the modules page for more information)
• Both single threaded and MPI
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • $LOCSCALE_HOME
• Example files in $LOCSCALE_EXAMPLE

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load LocScale

[user@cn3144 ~]$ cp $LOCSCALE_EXAMPLE/{pdb3j5p.pdb,emd5778_mask.mrc,emd_5778.map} .
[user@cn3144 ~]$ prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778.map -ma emd5778_mask.mrc

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. LocScale.sh). For example:

#!/bin/bash
set -e
module load LocScale
prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778.map -ma emd5778_mask.mrc
mpirun -np $SLURM_NTASKS locscale_mpi.py -em emd_5778_4locscale.mrc -mm pdb3j5p_4locscale.mrc -ma emd5778_mask_4locscale.mrc -p 1.2 -w 10 -mpi -o scaled.mrc

Submit this job using the Slurm sbatch command.

sbatch --partition=multinode [--ntasks=#] LocScale.sh

where # is the number of CPUs, e.g. 8.