PROCHECK-NMR parameters

4-9. Dihedral angle frequency distributions

The Dihedral angle frequency distribution plots cover the following dihedral angle distributions:-

• 4. Residue Phi torsion angle plots
• 5. Residue Psi torsion angle plots
• 6. Residue Chi-1 plots
• 7. Residue Chi-2 plots
• 8. Residue Ramachandran plots
• 9. Residue chi1-chi2 plots

The 14 parameters are as follows:-

4-9. Dihedral angle frequency distributions
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Y     <- Plot histograms, rather than show successive values (Y/N)?
0.0   <- Circ. var. cut-off (residues with lower values not plotted)
Y     <- Background shading (Y/N)?
N     <- Produce a COLOUR PostScript file (Y/N)?
WHITE        <- Background colour of page
CREAM        <- Background colour on graphs
CYAN         <- Shading of region representing dihedral angle restraints
YELLOW       <- Colour for favourable G-factor scores
RED          <- Colour for unfavourable G-factor scores
YELLOW       <- Colour for accessibility & circular variance dials
N     <- Omit circular variance value and dial (Y/N)?
N     <- Omit G-factor value and shaded square (Y/N)?
N     <- Omit accessibility symbol (Y/N)?
N     <- Splay model-numbering on the 2D plots (Y/N)?

Description of options:-

• Plot histograms, rather than show successive values (Y/N)? - The first option selects whether each dihedral angle distribution is to be plotted as a histogram or a "progression" of successive values. The former shows any clustering of dihedral angles around a given point, while the latter shows how the values change from model to model and can help identify in which models the values may be unusual.

• Circ. var. cut-off (residues with lower values not plotted) - This parameter allows you define a circular variance cut-off to show only those residues whose circular variance is above the given value. This can highlight residues with a scattered range of values for the given dihedral angle. The circular variance varies from 0.0 to 1.0, the lower the value the more clustered the dihedral angles.

• Background shading (Y/N)? - This option applies only for black-and-white plots and defines whether the graph-box in which the data are plotted is shaded a light grey or is left white.

• 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.

• Background colour on graphs - This defines the background colour of each graph box within which the data are plotted.

• Shading of region representing dihedral angle restraints - Where dihedral angle restraints have been applied, the range defining the restraint limits is shown in the colour defined here, allowing you to see how the actual values fall within (or outside) the range. If, for example, the values all cluster at the extreme edge of the range, this may suggest that the structures are being strained at this residue and the restraint values are incorrect, or are inconsistent with other restraints applied.

• Colours - The various additional colours on the lines that follow define the colour ranges for G-factors, and the colour for the schematic diagram of the secondary structure and the accessibility and circular variance dials.

• Omit circular variance, G-factor and/or accessibility symbol - These option define whether the symbols shown on each of the graphs for the various properties of that residue should be included or omitted.

• Splay model-numbering on the 2D plots - This option applies only to the 2D plots, namely the Residue Ramachandran plots and the Residue chi1-chi2 plots. It splays out all the model numbers from their corresponding data points to allow you to see where on the plot each model's data point is, as in the example given below.