Biowulf High Performance Computing at the NIH
LocScale on Biowulf

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.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

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

Batch job
Most jobs should be run as batch jobs.

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

set -e
module load LocScale -mc pdb3j5p.pdb -em -ma emd5778_mask.mrc
mpirun -np $SLURM_NTASKS -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=#]

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