PROCHECK-NMR parameters

13-14. Distance restraints and Restrain differences plots

These parameter cover the two plots:-

• 13. Distance restraints plot, and
• 14. Restraint differences plot

The 14 parameters are as follows:-

13-14. Distance restraints and Restrain differences plots
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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     <- Show only violated restraints (Y/N)?
Y     <- Exclude duplicate restraints within the same residue (Y/N)?
Y     <- Background shading on main graphs (Y/N)?
N     <- Produce a COLOUR PostScript file (Y/N)?
WHITE        <- Background colour
CREAM        <- Background shading on main graphs
PINK         <- Shading for regions outside upper restraint bounds
ORANGE       <- Shading for regions outside lower restraint bounds

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.

• Show only violated restraints - This option determines whether only violated restraints are to be included in the plots. If the option is set to N, then all restraints will be shown.

• Exclude duplicate restraints within the same residue - This option determines whether each intra-residue restraint is to be shown once only, or is to be included twice - once for each atom. (ie whether the restraint between atoms 2HB and 2HD2 of Asn should be shown once only, or both as 2HB->2HD2 and as 2HD2->2HB.

• Background shading (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.

• 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 additional colours define how the regions of the graphs outside the upper- and lower- restraints bounds are to be coloured.