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8. Viewing restraint violations in 3D

A simple utility program called viol2pdb is provided with PROCHECK-NMR to allow you to visualize in 3D a given structure's distance restraints and their violations.

The program generates two output files, in PDB format, for each of the following sets of distance restraints:-

One file of each pair contains the satisfied distance restraints while the other contains those that are violated. Viewing these PDB files in a molecular graphics program (such as QUANTA or RasMol), perhaps superimposed on your molecule, can identify which regions are poorly defined and which contain significant numbers of restraint violations.

Various options allow you to specify which types of restraints and violations you want extracted.


 Violated restraints  Satisfied restraints

Running viol2pdb

Before running viol2pdb you must first run AQUA to compute all the restraint violations in your structure and generate all the files that viol2pdb requires.

Then, to run viol2pdb, enter:



For example,

would run viol2pdb on Model 2 of the file 1nmr.pdb, extracting all the long- and medium-range restraints.

The following command:

would run viol2pdb on 1nmr.pdb using the models and residue ranges defined in the ranges file 1nmr.ranges. Only long-range restraints would be included.

Output PDB files

Each run of viol2pdb generates 6 output PDB files, as follows:-
                       Satisfied              Violated         
       NOE:        1nmr_noesatis.pdb     1nmr_noeviol.pdb 
       H-bond:     1nmr_hbsatis.pdb      1nmr_hbviol.pdb  
       S-S:        1nmr_sssatis.pdb      1nmr_ssviol.pdb  

where the name of the original PDB file is 1nmr.pdb.

When viewed in QUANTA or RasMol the resultant sets of "bond-lines" should show the following:-

Note that, other molecular graphics packages may show the restraints in colours that are different from those described above. Also, there may be problems with the way that the restraint lines themselves are linked by the program's "bonding algorithm" (see below).

Viewing the restraints

The restraints can be viewed by loading any, or all, of the PDB files output by viol2pdb into a standard molecular graphics package such as QUANTA or RasMol.

The line-segments corresponding to the red, white and blue lines described above are obtained by "bonds" between oxygen, hydrogen and nitrogen "atoms" in the PDB files created by viol2pdb. All the atoms are defined in HETATM records and the linkages between them are defined in the CONECT records at the end of the file.

For this reason, it is important that the molecular graphics package uses only the CONECT records in determining which "atoms" are "bonded". If it uses its own algorithm (eg on the basis of distances or residue types) the resultant set of bonds will not give the desired result.

Therefore, you may need to switch off the package's standard bonding algorithm when loading in the PDB files generated by viol2pdb.

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