PROCHECK-NMR parameters

General parameters for restraint plots

The General parameters apply to all the plots that show restraints and restraint violations. The parameters define how the restraints are to be classified and coloured.

The restraints are classified into 3 groups: Short, Medium and Long. The default classification is according to sequence separation, as follows:-

• Short-range - restraint is between atoms of same residue
• Medium-range - restraint links residues whose sequence separation is between i + 1 and i + 4
• Long-range - restraint links residues whose sequence separation is greater than 4 residues

An alternative classification is on the basis of distance ranges. So, short-range restraints might be defined as those whose length is 0.0 to 3.5 Ångstroms, medium-range as 3.5 to 5.0 Ångstroms, etc.

The 7 parameters are:-

General parameters
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N     <- Define short/medium/long-range restraints by dist (Y/N)?
0.0  3.5     <- Upper and lower distance defining short-range restraints
3.5  5.0     <-   "    "    "      "        "     medium-range     "
5.0 10.0     <-   "    "    "      "        "     long-range     "
YELLOW       <- Colour for long-range restraints
LIME GREEN   <- Colour for medium-range restraints
CYAN         <- Colour for short-range restraints

Description of options:-

• Define short/medium/long-range restraints by dist - The first option defines whether the restraints are to be classified according to distance or sequence separation.

• Distance ranges - The distance ranges define the classification of restraints into short-range, medium-range and long-range, and are only used if the option above is set to Y.

• Colours - The colours define the colouring of the short-, medium- and long-range restraints.