PROCHECK-NMR parameters

19-21. Restraint spans, residue-by-residue and model-by-model violations

These parameter cover the three plots:-

• 19. Restraint spans
• 20. Residue-by-residue restraint violations, and
• 21. Model-by-model violations

The 19 parameters are as follows:-

19-21. Restraint spans, residue-by-residue and model-by-model violations
------------------------------------------------------------------------
Y     <- Include all short-range restraints (as defined above) (Y/N)?
Y     <-    "     "  medium-range     "      "     "      "    (Y/N)?
Y     <-    "     "  long-range       "      "     "      "    (Y/N)?
Y     <- Include NOE distance restraints (Y/N)?
Y     <- Include H-bond distance restraints (Y/N)?
Y     <- Include disulphide distance restraints (Y/N)?
Y     <- Background shading on main graphs (Y/N)?
Y     <- Show shading representing estimated accessibility (Y/N)?
N     <- Produce a COLOUR PostScript file (Y/N)?
WHITE        <- Background colour
CREAM        <- Background shading on main graphs
BLUE         <- Minimum accessibility colour (buried regions)
WHITE        <- Maximum accessibility colour
YELLOW       <- Colour for favourable G-factor scores
RED          <- Colour for unfavourable G-factor scores
YELLOW       <- Colour for schematic of the secondary structure
YELLOW       <- Colour for accessibility dials
CYAN         <- Colour for histograms of restraints per residue
RED          <- Colour for restraint violations

Description of options:-

• Include all short-range, medium-range and long-range restraints - The first 3 options define which restraint classes are to be included in the plots.

• Include NOE, H-bond and disulphide restraints - The next 3 options define which types of restraints - whether NOE, hydrogen-bond and S-S disulphide restraints - are to be included in the plots.

• Background shading on main graphs (Y/N)? - This option applies only for black-and-white plots and defines whether the graph-box in which the data are plotted is shaded a light grey or is left white.

• Show shading representing estimated accessibility - This option determines whether the secondary structure diagram is to be plotted on a shaded background in which the shading shows the buried and accessible regions of the structure. At present the accessibility is crudely estimated from each residue's Ooi number.

• Produce a COLOUR PostScript file - This option defines whether a colour or black-and-white plot is required. Note that if the Colour all plots option is set to Y, a colour PostScript file will be produced irrespective of the setting here.

  The colour definitions on the following lines use the `names' of each colour as defined in the colour table at the bottom of the parameter file (see Colours). If the name of a colour is mis-spelt, or does not appear in the colour table, then white will be taken instead. Each colour can be altered to suit your taste and aesthetic judgement, as described in the Colours section.

• Background colour - This option defines the background colour of the page on which the plots are drawn.

• Colours - The various additional colours on the lines that follow define the colours for the background colour of the graphs, the colour range for buried and accessible residues, colour ranges for G-factors, colour for the schematic diagram of the secondary structure, the colour of the accessibility and circular variance dials, and the colours of the histogram bars and restraint violations.