PROCHECK-NMR Operating Manual

2. How to run AQUA and PROCHECK-NMR

Step 1. Check PDB format.
Before running AQUA or PROCHECK-NMR, check that your coordinates are in PDB format, with each model bounded by MODEL and ENDMDL records (see PDB format).

If the models are all in separate PDB files, you can use the AQUA script, joinpdb (see Appendix C), to merge them into a single PDB file.

Note that if you are only running AQUA, the coordinates can be in BIOSYM format.

Step 2. Run qconvert

This converts your restraints file into the AQUA format for analysis of restraint violations. At present, the following file formats for distance and torsion angle restraints can be interpreted: DISGEO, X-PLOR, BIOSYM, DISMAN/DIANA. Other formats may be converted by supplying a script, see Restraint conversion.
qconvert [-r restraint_prefix] [-t file_type] restraint_file

(If you have no restraints file, or it cannot be converted, skip to step 4).

Step 3. Run AQUA

This analyzes the restraint violations of a given set of distance and torsion angle restraints.
aqpc [-c] [-r restraint_prefix] coordinate_file [ranges-file]

Step 4. Run PROCHECK-NMR

This produces PostScript plots to highlight the restraint violations between the models and the restraint data (as computed by AQUA), and also various analyses of the geometry of the structures in the ensemble.
procheck_nmr coordinate_file [ranges-file]

Additionally, you might want to:-

• Re-run AQUA and/or PROCHECK-NMR for only selected models and/or residues. You can list which models and/or residues are to be included in the analyses and plots in a simple ASCII text file (see Selecting model- and residue-ranges).

• Regenerate the PROCHECK-NMR plots using different plot parameters. You can edit the procheck_nmr.prm parameter file to alter the appearance, and information plotted, on some of the plots (see Customizing the PROCHECK-NMR plots). You re-run the plots using proplot_nmr.

• Run the standard single-model PROCHECK on any one of the models in your ensemble to get the additional analyses that provides (eg analysis of main chain bond lengths and angles, analysis of planar groups, full output listing of all geometrical parameters).

• View the restraints and restraint violations in 3D using viol2pdb to generate PDB-format files which can then be displayed and viewed using standard molecular modelling software.

PROCHECK-NMR Operating Manual