10. Ensemble geometry
There are 15 parameters defining the
Ensemble geometry, as follows:-
10. Ensemble geometry
1 2 < Which 2 main graphs to be printed
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
YELLOW <- Colour for favourable G-factor scores
RED <- Colour for unfavourable G-factor scores
YELLOW <- Colour for schematic of the secondary structure
YELLOW <- Colour for accessibility & circular variance dials
Description of options:-
- Which 2 main graphs to be printed - The first option
defines which 2 out of the 3 possible graphs are to appear as
the main graphs on the plot. The 3 possibilities available at
- Absolute deviation from mean Chi-1 value (excl. Pro)
- Absolute deviation from mean of omega torsion
- C-alpha chirality: abs. deviation of zeta torsion
Entering 0 for any of the 2 options will leave a blank region
in place of a graph at the corresponding position on the page.
- Background shading on main graphs - This option applies only for
black-and-white plots and defines whether the graph-boxes in which the data
for the 2 main plots are plotted is shaded a light grey or is left white.
- Number of standard deviations for highlighting - This option
determines which histogram bars in the 2 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 representing estimated 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 crudely estimated
from each residue's Ooi number.
- 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 background colour of the graphs, the colours of
the histogram bars on the graphs, colour ranges for G-factors, colour for
the schematic diagram of the secondary structure, and the colour of the
accessibility and circular variance dials.