PROCHECK-NMR - Sample plots
4. Residue Phi torsion angle plots
Description
The Residue Phi torsion angle plots show how the phi dihedral
angles vary for each residue across the different members of the NMR
ensemble. (The values can also be plotted as a "progression" of
values, as is shown for chi-1 here).
Where any of the residues have had restraints applied to the
dihedral angle, the ranges of these are shown on the plots as the
darker bands. The numbers of violations of these restraints, if any, are
printed on the plot.
It is sometimes possible to see how the values cluster at the borders of
these restraint ranges, as though trying to escape from the range,
suggesting that maybe the range itself may be incorrect.
The top right-hand corner of each residue's graph shows:-
- The circular variance, both as a
value (between 0.0 and 1.0) and as a symbol (the lower the
value the smaller the black segment on the dial).
- A dial representing the residue's estimated accessibility. The
darker the dial, with more spokes protuding, the more
solvent-accessible the residue is. At present the
accessibility is crudely estimated from each residue's Ooi number.
Options
The main options for the Residue Phi torsion angle plots are:-
- The dihedral angles can be plotted as a "progression" of values,
rather than as the histograms shown above. The progression shows how
the values change from one model to the next, which may help in identifying
which models contain the outliers.
- Plot of only those residues with a wide spread of torsion angles
(as defined by a cut-off on the circular
variance value).
- The plot can be in colour or black-and-white.
These options can be altered by editing the parameter file,
procheck_nmr.prm, as described here.
PROCHECK-NMR - Sample plots