PROCHECK parameters

1. Ramachandran plot

There are 14 parameters defining the Ramachandran plot, as follows:-

1. Ramachandran plot
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Y     <- Shade in the different regions (Y/N)?
Y     <- Print the letter-codes identifying the different regions (Y/N)?
Y     <- Draw line-borders around the regions (Y/N)?
N     <- Show only the core region (Y/N)?
1     <- Label residues in: 0=disallow,1=generous,2=allow,3=core regions
N     <- Produce a COLOUR PostScript file (Y/N)?
WHITE        <- Background colour
WHITE        <- Region 0: Disallowed
CREAM        <- Region 1: Generous
YELLOW       <- Region 2: Allowed
RED          <- Region 3: Most favourable, core, region
BLACK        <- Colour of markers in favourable regions
RED          <- Colour of markers in unfavourable regions
N     <- Produce "publication version" of Ramachandran plot (Y/N)?

Description of options:-

• Shade in the different regions - The second option defines whether the different regions of the Ramachandran plot are to be shaded in.

  Without shading, the regions can still be made out if their borders are drawn in (see Draw line-borders around the regions). In black-and-white, the shading shows the most favourable regions in the darkest grey, with the less favourable regions being shown in progressively lighter tones. If you are only interested in the core region, then set the option Show only the core region below to Y.

• Print the letter-codes identifying the different regions - The next option defines whether the different regions of the Ramachandran plot are to be labelled using the appropriate codes: A, B, L, etc.

• Draw line-borders around the regions - This option defines whether borders are drawn round the different regions of the Ramachandran plot. If you are only interested in the core region, then set the option Show only the core region below to Y.

• Show only the core region - This option defines whether only the core regions (ie the most favoured regions: A, B, and L) of the Ramachandran plot are to be outlined and/or shaded. This gives an easy-to-see guide as to how many residues are inside and outside the cores.

• Label residues in: 0=disallow,1=generous,2=allow,3=core - This option defines which residues are labelled on the Ramachandran plot. Option 0 labels only the residues in the ``disallowed'' regions. Option 1 labels residues in the disallowed and ``generous'' regions. And so on. In all cases, Gly residues are left unlabelled and are identified by a triangular marker.

• 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 colour of each of the 4 different regions on the Ramachandran plot, and the colours of the markers that are located in the favourable and unfavourable regions.

• Produce "publication version" of plot - This option allows you to plot just the Ramachandran plot with no border around the edges and none of the statistics below it, as would be suitable for publication. An example is given here.

PROCHECK parameters