2. PLOT PARAMETERS

There are 18 PLOT PARAMETERS, as follows:-

PLOT PARAMETERS
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Y     <- Include: Hydrophobic interactions - (Y/N)?
N     <- Include: Water molecules - (Y/N)?
Y     <- Include: Non-ligand mainchain atoms - (Y/N)?
Y     <- Include: Linked residues listed below - (Y/N)?
Y     <- Plot: Hydrogen bonds - (Y/N)?
N     <- Plot: Internal H-bonds in ligand - (Y/N)?
Y     <- Plot: External groups covalently bonded to ligand - (Y/N)?
N     <- Plot: Bonds showing hydrophobic interactions - (Y/N)?
N     <- Plot: Schematic ligand representation [see Note 1] - (Y/N)?
N     <- Plot: Schematic non-ligand residues [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)?
Y     <- Plot: Solid lines for covalent bonds to external groups - (Y/N)?
0     <- Non-bonded contacts option [see Note 3]
Y     <- Plot: Water atoms (as spheres) - (Y/N)?
Y     <- Plot: Accessibility shading for the ligand only - (Y/N)?

Description of the parameters:-

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: External groups covalently bonded to ligand - (Y/N)? This option defines whether residues that are not part of the ligand, but which are covalently bonded to it, are to be included in the plot.

Plot: Bonds showing hydrophobic interactions - (Y/N)? This option defines whether dotted lines are to be drawn between atoms involved in hydrophobic contacts. Normally, the LIGPLOT diagram only gives short spokes radiating from each atom involved in such a contact, the direction of the spokes being towards its contacting partner. But if you want to see in detail which pairs of atoms are involved, set this option to "Y".

Plot: Schematic 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 at the C-alpha position. Ligand sidechains not involved in either hydrogen bonds nor non-bonded contacts are not shown.

Plot: Schematic non-ligand residues - (Y/N)? This option represents non-ligand residues by a single box containing the residue name, number and chain identifier.

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 (see section 2c - Showing atom accessibilities computed by NACCESS on how to add the accessibility shadings to your plot).

Note that, if LIGPLOT is run on an ordinary PDB file with this option set to Y, the shading will use the values in the B-factor column.

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:-

First, run LIGPLOT in the usual manner.
Then, edit the ligplot.bonds file and change the "s" in the final column of any double-bond to "d", and, for any triple-bond, to "t".
Finally, re-run LIGPLOT for the ligplot.pdb file (and not the original PDB file - ie run: ligplot ligplot.pdb [options], where the options defining the ligand are as before).

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.

Plot: Solid lines for covalent bonds to external groups - (Y/N)? If you have opted to include residues that are not part of the ligand, but which are covalently bonded to it, this option allows you define whether the covalent bonds between ligand and residue are to be shown as dotted or solid lines. The colour and thickness of these lines can be separately set in the SIZES and COLOURS parameters.

Non-bonded contacts option The non-bonded contacts option determines which non-bonded contacts are to be included in the plot. The options are:-

0. Only contacts between hydrophobic atom types (ie carbon/sulphur atoms in contact with other carbon/sulphur atoms). This is how LIGPLOT defined hydrophobic contacts in versions prior to v.3.2.

1. A contact between a carbon/sulphur atom and any other atom.

2. A contact between any pair of atoms - excluding those that are hydrogen-bonded.

The distance defining an atom-atom contact is specified by the parameters to HBPLUS in ligplot.scr and can be changed there if necessary.

Plot: Water atoms (as spheres) - (Y/N)? This option defines whether the water atoms (if included in the plot) are to be shown as spheres. If this option is set to N, only the hydrogen bonds to the waters will be shown.

Plot: Accessibility shading for the ligand only - (Y/N)? If accessibility shading is switched on (via the Accessibility shading parameter above) this option defines whether the shading is to apply to only the ligand atoms or to the non-ligand atoms as well.