PROCHECK-NMR - Sample plots
PROCHECK-NMR - Sample plots
The Residue-by-residue restraint violations shows a summary of each residue's restraint violations.
The different plots show:-
This plot shows each residue's highest upper-bound distance violation in each model in the ensemble. The corresponding model number is shown inside each data point.
The shape of each data point corresponds to the type of distance restraint, as follows:-
The colour of each data point corresponds to the class of distance restraint, as defined in the General parameters. The restraints are also labelled L, M or S according to this class (ie Long, Medium or Short).
This plot shows the sum of each residue's upper-bound distance violations. The totals from each model are stack on top of each other. Thus the higher the stack, the greater the overall violation of that residue's restraints across all the models of the ensemble.
The number shown at the top of each stack corresponds to the model number having the highest total violation for that residue.
The secondary structure plot shows a schematic representation of the Kabsch & Sander (1983) secondary structure assignments. The key just below the picture shows which structure is which. Beta strands are taken to include all residues with a Kabsch & Sander assignment of E, helices corresponds to both H and G assignments, while everything else is taken to be random coil.
The shading behind the schematic picture gives an approximation to the residue accessibilities. The approximation is a fairly crude one, being based on each residue's Ooi number (Nishikawa & Ooi, 1986). An Ooi number is a count of the number of other Calpha atoms within a radius of, in this case, 14Å of the given residue's own Calpha. Although crude, this does give a good impression of which parts of the structure are buried and which are exposed on the surface. Future versions of PROCHECK will include an accurate calculation of residue accessibility.
This histogram shows a simple representation of the numbers of distance restraints that each residue has. The number at the top of the stack gives this number. Intra-residue restraints are counted once only to give this number, and how many there are of them is shown in brackets just below.
The highlighted regions illustrate the numbers of violated restraints. The regions are made up of horizontal bars stacked on top of one another, each bar corresponding to a violated restraint. The width of the highlighted region of each bar is proportional to the number of models in which the restraint is violated. The restraints violated in the largest number of models are shown at the bottom. The higher bars correspond to those restraints violated in fewer and fewer numbers of models, and so stretch across only part of the width.
Below the histograms are small bars corresponding to each dihedral angle restraint. As before, the degree of highlighting of each bar corresponds to the number of models in which the restraint is violated.
The main options for the Residue-by-residue restraint violations are:-
These options can be altered by editing the parameter file, procheck_nmr.prm, as described here.
PROCHECK-NMR - Sample plots