N U C P L O T manual

5. Altering the appearance of the plot

The resulting plots can be altered by changing the plot parameters in the parameter file "nucplot.par which can be found in the current directory. When running NUCPLOT in a new directory, the default parameter file is copied from the nucplot directory. To return to the default parameters for the plot, simply remove the parameter file from the working directory and run the NUCPLOT script. The file can be edited with any text editor.

a) Print options:

• Produce a colour PostScript file (Y/N)? - Defines whether the diagram is drawn in colour or black and white.
  
  
• Orientation of plot: (P)ortrait or (L)andscape? - Defines whether the orientation of the plot is to be portrait or landscape.
  
  
• Plot title (Y/N)? - Defines whether the PDB filename is shown on the plot as a title.
  
  
• Show key to plot (Y/N)? - Defines whether the key to the symbols on the plot are shown.
  
  
• Output filename = "nucplot.ps" (Y/N)? - Defines whether the output filename is nucplot.ps. The alternative format is pdbname_X.ps where pdbname is the name of the input file and X is the chain ID of the first DNA chain on the plot.
  
  

b) Plot parameters:

• Read bonding information from .bond file (Y/N)? - Defines whether the protein-DNA, water-DNA, and protein-water-DNA interaction information is read from a file in .bond format. A file listing all the interactions shown on the plot is automatically produced by NUCPLOT. This can be edited and used as an input if the you wish to display certain interactions only.
  
  
• Include protein residue H-bonds (Y/N)? - Defines whether protein-DNA hydrogen bonds should be included in the plot.
  
  
• Include non-bridging water H-bonds (Y/N)? - Defines whether non-bridging water-DNA hydrogen bonds should be included in the plot.
  
  
• Include bridging water H-bonds (Y/N)? - Defines whether protein-bridging water-DNA hydrogen bonds should be included in the plot.
  
  
• Include non-bonded contacts (Y/N)? - Defines whether van der Waals interactions should be included in the plot.
  
  
• Use one-letter amino acid codes for protein residue names (Y/N)? - Defines whether the residue names shown on the plot are represented by the single or three letter code.
  
  
• Residues only, rather than all atoms, for non-bonded contacts (Y/N)? - Defines whether the atom name is shown for the van der Waals bonds. Showing only residue names reduces crowding on the plot.
  
  

c) Numerical parameters:

• Number of base pairs on each page - Defines the number of base pairs to be placed on each page.
  
  
• Distance cut off for hydrogen bonds - Defines the cut off distance for hydrogen bonds. Bonds must be below this length to be displayed on the plot. The maximum distance allowed is 3.35Å. More details.
  
  
• Distance cut off for non-bonded contacts - Defines the cut off distance for van der Waals bonds. Maximum distance allowed is 3.90Å. More details.
  
  

d) Colour parameters:

The colours of the background and various symbols of the plot can be defined. The definitions of the different colours are described below. The colour name must be one that is defined in the list of colour definitions.

e) Colour definitions:

The colour definitions table allows you to modify any of the default colour definitions. You canalso set up new colours of your own (up to 20 different colours are allowed).

Each entry contains three numbers, each between 0.0 and 1.0, giving the ratios of red, green and blue, respectively, making up the given colour.

Each colour has a name defined within the single quotes and may be altered. These names are referred to when assigning colours in the "Colour parameters" section (see above section).

f) Non-standard bases:

The list allows you to include non-standard bases in the plot. New base types may be added by appending the name to the list as it appears in the PDB.

N U C P L O T manual