There are 16 PLOT PARAMETERS, as follows:-
PLOT PARAMETERS --------------- Y <- Include: Hydrophobic interactions - (Y/N)? N <- Include: Water molecules - (Y/N)? Y <- Include: Non-ligand mainchain atoms - (Y/N)? N <- Include: Linked residues listed below - (Y/N)? Y <- Plot: Hydrogen bonds - (Y/N)? N <- Plot: Internal H-bonds in ligand - (Y/N)? N <- Plot: Simple ligand representation [see Note 1] - (Y/N)? N <- Plot: Accessibility shading [see Note 2] - (Y/N)? Y <- Plot: Ligand atoms (as spheres) - (Y/N)? Y <- Plot: Nonligand atoms (as spheres) - (Y/N)? Y <- Plot: Double- and triple bonds (for ligplot.pdb only) - (Y/N)? Y <- Print: Key to symbols in PostScript output - (Y/N)? Y <- Print: Residue names/numbers - (Y/N)? Y <- Print: Atom names - (Y/N)? Y <- Print: H-bond lengths on hydrogen bonds - (Y/N)? Y <- Print: Filename as title if title not explicitly defined - (Y/N)?
Include: Hydrophobic interactions - (Y/N)? The first option defines whether all hydrophobic interactions between the protein and the ligand are to be shown on the plot.
Include: Water molecules - (Y/N)? The second option defines whether any water molecules hydrogen-bonded to the ligand are to be shown on the plot.
Include: Non-ligand mainchain atoms - (Y/N)? This option defines whether the mainchain atoms of the non ligand residues are to be shown on the plot.
Include: Linked residues listed below - (Y/N)? This option allows you to include any residues that are not directly hydrogen-bonded to the ligand but which are indirectly connected via another residue (or water molecule) which is hydrogen-bonded to the ligand.
For example, in the enzyme active sites of the serine proteases the His-Asp pair is essential for catalytic activity. Here the His is hydrogen bonded to the ligand whereas the Asp is hydrogen bonded to the His and not to the ligand (as for His 57 and Asp 102 in chymotrypsin). By setting the Linked residues to Y here, you can then define which linked residues you want included in the plot (see LINKED RESIDUES).
Plot: Hydrogen bonds - (Y/N)? This option defines whether hydrogen bond interactions between the ligand and the protein are to be shown on the plot.
Plot: Internal H-bonds in ligand - (Y/N)? This option defines whether internal hydrogen bonds within the ligand itself are to be shown on the plot. Generally, however, these comlicate the diagram unnecessarily.
Plot: Simple ligand representation - (Y/N)? This option may be useful if the ligand is large (for example a peptide). It prints out the ligand residues as circles and the non ligand residues just have their names and atom identifiers printed out. Ligand sidechains not involved in hydrogen bonds are not shown.
Plot: Accessibility shading - (Y/N)? This option defines whether the solvent accessibilities of the ligand atoms are to be shown on the plot. The accessibilities are represented by the shading behind each ligand atom. Solvent accessibilities can be calculated by running the NACCESS program. This generates an .asa file, and LIGPLOT should then be run on this .asa file in place of the original .pdb file. (If LIGPLOT is run on an ordinary PDB file, the values in the B-value column will be taken to be accessibilities).
Plot: Ligand atoms (as spheres) - (Y/N)? This option defines whether the ligand atoms are to be shown on the plot (if this option is set to N, only the ligand bonds will be shown).
Plot: Nonligand atoms (as spheres) - (Y/N)? As above, but for the non-ligand atoms.
Plot: Double- and triple-bonds - (Y/N)? This option defines whether double- and triple-bonds are to be plotted. At present, LIGPLOT assumes that all bonds are single bonds and needs to be told which are double and which are triple. This is done as follows:-
Print: Key to symbols in PostScript output - (Y/N)? This option defines whether a key explaining the symbols used in the LIGPLOT diagram produced is to be included in the plot.
Print: Residue names/numbers - (Y/N)? This option defines whether residue names and numbers are to be printed adjacent to the relevant residues.
Print: Atom names - (Y/N)? This option defines whether atom names are to be printed next to each of the atoms.
Print: H-bond lengths on hydrogen bonds - (Y/N)? This option defines whether the length of each hydrogen bond is to be printed on the plot.
Print: Filename as title if title not explicitly defined - (Y/N)? If the -h option is omitted when LIGPLOT is run, the program will not prompt for a title for the plot. In which case, if the "Filename as title" option is set to "Y", the filename will be printed as the plot title instead.