PROCHECK-NMR parameters
2. Gly & Pro Ramachandran plots
There are 8 parameters defining the
Gly & Pro Ramachandran plots, as follows:-
2. Gly & Pro Ramachandran plots
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-3.0 <- Cut-off value for labelling of residues
N <- 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
BLACK <- 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.
- 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.