Biowulf High Performance Computing at the NIH
PROCHECK on Biowulf

The aim of PROCHECK is to assess how normal, or conversely how unusual, the geometry of the residues in a given protein structure is, as compared with stereochemical parameters derived from well-refined, high-resolution structures.

Unusual regions highlighted by PROCHECK are not necessarily errors as such, but may be unusual features for which there is a reasonable explanation (eg distortions due to ligand-binding in the protein's active site). Nevertheless they are regions that should be checked carefully.

References:

Documentation
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@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 PROCHECK
[user@cn3144 ~]$ procheck my.pdb 2.5

[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. PROCHECK.sh). For example:

#!/bin/bash
module load PROCHECK
procheck my.pdb 2.5

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] PROCHECK.sh