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:

• Laskowski R A, MacArthur M W, Moss D S & Thornton J M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. (1993), 26, 283-291.

• PROCHECK Main Site
• Online Manual

• Module Name: PROCHECK (see the modules page for more information)
• environment variables set
  • prodir
  • aquaroot
  • AQUABINDIR
  • AQUADATADIR
  • AQUADOCDIR
  • AQUAEXMPLSDIR
  • AQUAEXTRASDIR
  • AQUAHELPLIST
  • AQUAHELPPRINT
  • AQUASCRIPTSDIR
  • AQUASRCDIR
  • AQUAVERS

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 ~]$

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