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6. Improving the plots

The plots produce by LIGPLOT can be improved in one of two ways.

a. Editing the PostScript file

The file is an ASCII text file, and so can be modified using any text editor. The sorts of amendments you can make are: changes to labels (in terms of size, colour and text), addition of other text, changes to colours, sizes, etc.

Some changes, of course, can be made simply by altering the ligplot.par parameter file (see section 5) and re-running LIGPLOT.

b. Editing the ligplot.pdb file using interactive computer graphics software

The ligplot.pdb file contains the coordinates of the flattened molecules, exactly as seen on the plot. You can read it in as a standard PDB file and then use standard molecular modelling operations to modify the structure in any way that will make the final plot clearer.

For example, if you are using QUANTA, you might modify the plot as follows:-

1. First, import the ligplot.pdb file as a PDB file.

2. Then, use the "Distance" option of the "Geometry" panel to add dotted lines between hydrogen-bonded atoms. Click first on one, and then the other, of each hydrogen-bonded atom pair. A dotted line will be drawn between the two atoms, showing their distance apart in Angstroms. This will reproduce the hydrogen bonds shown on the LIGPLOT diagram, and will be useful in getting the distances between them to match the actual distances (printed on the plot) as closely as possible.

3. Use the "Move Fragment" option of the "Modelling" panel to manually move any of the non-ligand residues around the screen.

   Note that the residues corresponding to hydrophobic contacts will be represented by one (or sometimes more) single carbon atoms. These, too, can be moved around the screen to more favourable positions.

4. Use the "Torsions" option of the "Modelling" panel to rotate any of the residues or sidechains about any of their rotatable bonds. You can use the torsion angle monitors to ensure that the final torsion angle is always either 0 or 180 degrees (otherwise the molecule will lose its flatness, and subsequent operations may result in greater and greater distortions to the final picture).

5. Once all the required amendment have been made, save the file as ligplot.pdb, overwriting the previous version. (See note below).

6. Re-run LIGPLOT, this time using ligplot.pdb as the input file (ie run: ligplot ligplot.pdb [options], where the options defining the ligand are as before). This should produce a new LIGPLOT diagram with all residues laid out as defined on screen.

Note that, when the ligplot.pdb file is saved by QUANTA, any blank chain ID's are replaced by the chain identifier "A". In this case, the residues in the ligplot.pdb file will no longer match the data in the ligplot.hhb, ligplot.nnb and ligplot.bonds files.Thus you will need to edit ligplot.pdb to convert the chain "A" back to chain " " (blank).