PROCHECK parameters

2. Gly & Pro Ramachandran plots

There are 8 parameters defining the Gly & Pro Ramachandran plots (which by default actually print Ramachandrans for each of the 20 different residue types), as follows:-

2. Gly & Pro Ramachandran plots
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-3.0  <- Cut-off value for labelling of residues
Y     <- Plot all 20 Ramachandran plots (Y/N)?
N     <- Produce a COLOUR PostScript file (Y/N)?
WHITE        <- Background colour
CREAM        <- Lightest shaded regions on plots
GREEN        <- Darkest shaded regions on plots
YELLOW       <- Colour of markers in favourable regions
RED          <- Colour of markers in unfavourable regions

Description of options:-

• Cut-off value for labelling of residues - The first option defines the G-factor values below which residues on the Ramachandran plot will be labelled. The G-factor gives a measure of how far from the `normal' regions of the plot each residue lies. Low G-factors indicate residues in unlikely conformations.

• Plot all 20 Ramachandran plots - The second option allows you to show a separate phi-psi Ramachandran plot for each of the 20 different residue types, rather than just for Gly and Pro. The default setting is Y.

• 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 lightest- and darkest-shaded regions of the plot, and also the colours of the residue markers in the favourable and unfavourable regions.

PROCHECK parameters