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.
References:
- Jakobi AJ, Wilmanns M, Sachse C. Model-based local density sharpening of cryo-EM maps. Elife. 2017 Oct 23;6.
Documentation
Important Notes
- 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 $LOCSCALE_EXAMPLE
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ 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 $LOCSCALE_EXAMPLE/{pdb3j5p.pdb,emd5778_mask.mrc,emd_5778.map} . [user@cn3144 ~]$ 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 ~]$
Batch job
Most jobs should be run as batch jobs.
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.