PROCHECK parameters

10. Distorted geometry plots

There are 9 parameters defining the Distorted geometry plots, as follows:-

10. Distorted geometry plots
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0.05  <- Deviation from "ideal" bond-length (A)
10.0  <- Deviation from "ideal" bond-angle (degrees)
0.03  <- RMS distance from plane for ring atoms
0.02  <-  "      "      "    "   for other atoms
N     <- Produce a COLOUR PostScript file (Y/N)?
CREAM        <- Background colour of page
BLUE         <- Colour of "ideal" bond-lengths and angles
RED          <- Colour of actual bond-lengths/angles/planes
GREEN        <- Colour for lettering showing differences from ideals

Description of options:-

• Deviation from 'ideal' bond length (Å) - This option defines which main-chain bonds are to be plotted as distorted. All bond-lengths that deviate by more than this amount from the Engh & Huber 'ideal' values will be plotted.

• Deviation from 'ideal' bond angle (degrees) - This option defines which main-chain bond angles are to be plotted as distorted. All bond-angles that deviate by more than this amount from the Engh & Huber 'ideal' values will be plotted.

• RMS distance from plane - These two options defines which planar groups are to be plotted as distorted. All planar groups that deviate by more than this amount from planarity will be plotted. The two different values apply separately to ring groups (Phe, Tyr, Trp and His) and to planar end-groups (Arg, Asn, Asp, Gln and Glu).

• 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 'ideal' and actual bond lengths and angles and for the lettering showing the differences from the ideals.

PROCHECK parameters