PROCHECK parameters

6. Residue properties

There are 18 parameters defining the Residue properties plot, as follows:-

6. Residue properties
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1 2 3    < Which 3 main graphs to be printed (see Note 1 for full list)
Y     <- Background shading on main graphs (Y/N)?
2.0   <- Number of standard deviations for highlighting
Y     <- Show shading representing estimated accessibility (Y/N)?
N     <- Produce a COLOUR PostScript file (Y/N)?
WHITE        <- Background colour
CREAM        <- Background shading on main graphs
PURPLE       <- Colour of histogram bars on main graphs
RED          <- Colour of highlighted histogram bars
BLUE         <- Minimum accessibility colour (buried regions)
WHITE        <- Maximum accessibility colour
RED          <- Region 0: Disallowed
PINK         <- Region 1: Generous
GREEN        <- Region 2: Allowed
SKY BLUE     <- Region 3: Most favourable, core, region
YELLOW       <- Colour for favourable G-factor scores
RED          <- Colour for unfavourable G-factor scores
YELLOW       <- Colour for schematic of the secondary structure

Description of options:-

• Which 3 main graphs to be printed - This option defines which 3 out of the 14 possible graphs are to appear as the three main graphs at the top of the page. The 14 possibilities are:
  1. Absolute deviation from mean Chi-1 value (excl. Pro)
  2. Absolute deviation from mean of omega torsion
  3. C-alpha chirality: abs. deviation of zeta torsion
  4. Absolute deviation from mean of H-bond energy
  5. Gamma atom B-value
  6. Average B-value of main-chain atoms
  7. Average B-value of side-chain atoms
  8. G-factor for phi-psi distribution
  9. G-factor for chi1-chi2 distribution
  10. Residue-by-residue G-factor
  11. Approx. accessibility (estimated by Ooi numbers)
  12. Percentage residue main-chain accessibility
  13. Standard deviation of main-chain B-values
  14. Standard deviation of side-chain B-values
  

  Entering 0 for any of the 3 options will leave a blank region in place of a graph at the corresponding position on the page.

  By default, the first 3 graphs in the list will be plotted.

• Background shading - This option defines whether the background of each of the 3 main plots is to be lightly shaded when the plot is in black-and-white.

• Number of standard deviations for highlighting - This option determines which histogram bars in the 3 main plots are to highlighted. Residues whose plotted parameter deviates by more than the number of standard deviations specified here will be highlighted.

• Show shading for accessibility - This option determines whether the secondary structure diagram is to be plotted on a shaded background in which the shading shows the buried and accessible regions of the structure. At present the accessibility is estimated from each residue's Ooi number (Nishikawa & Ooi, 1986), but a proper accessibility calculation will be included in PROCHECK very soon.

• 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 for the different parts of the plot. These include the colouring of the 3 main graphs at the top of the plot, the accessibility shading and colour of the secondary structure diagram, the markers representing the different regions of the Ramachandran plot, and the range of colours used on the chequer-board of the various G-factors.

PROCHECK parameters