PROCHECK-NMR parameters

12. Model-by-model secondary structures

There are 6 parameters defining the Model-by-model secondary structures, as follows:-

12. Model-by-model secondary structures
---------------------------------------
Y     <- Show shading representing estimated accessibility (Y/N)?
N     <- Produce a COLOUR PostScript file (Y/N)?
WHITE        <- Background colour
BLUE         <- Minimum accessibility colour (buried regions)
WHITE        <- Maximum accessibility colour
YELLOW       <- Colour for schematic of the secondary structure

Description of options:-

• Show shading representing estimated accessibility - The first 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 minimum and maximum accessibilities, and the colour for the schematic diagram of the secondary structure.