Introduction

PROCHECK consists of 3 main components: the original PROCHECK programs for assessing the overall geometrical quality of protein structures, the extensions for analysing NMR ensembles (PROCHECK-NMR), and the version for comparing related protein structures (PROCHECK-COMP, or PROCOMP).

PROCHECK itself is intended as a tool for highlighting regions of a protein structure where the geometry is unusual and hence which may need closer examination.

PROCHECK-NMR is an extension for ensembles of NMR structures (where all models are in a single PDB file, delimited by MODEL and ENDMDL records). As well as analysing the geometry of the structures in the ensemble, the programs also produce analyses of the NMR restraint violations. The violations are calculated by a program called AQUA, written by Ton Rullmann of Utrecht University. AQUA requires the restraints be supplied in a standard file format, but also has scripts for converting DISGEO, X-PLOR, etc restraint files into this format. AQUA produces detailed listing of all its analyses.

PROCHECK-COMP is for comparing the residue-by-residue geometry of a set of closely-related structures, such as separate members of a family, or models of the same structure saved during different stages of refinement. It outputs a number of PostScript files showing the comparisons, including residue-by-residue Ramachandran plots and comparison of the different secondary structure elements in each PDB file.

IMPORTANT NOTE
For existing users, please note that the method of running the new PROCHECK-NMR programs has altered slightly in that the name of the restraints file is no longer required as the second parameter (which is now used for the ranges file instead - see Operating Instructions).