LIGPLOT v.4.0 - Parameter file (ligplot.prm) -------------------------------- PRINT OPTIONS ------------- Y <- Produce a colour PostScript file (Y/N)? P <- Orientation of plot: (P)ortrait or (L)andscape? 0.0 <- Rotation angle (clockwise) for final plot PLOT PARAMETERS --------------- 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)? Note 1 ------ In the "schematic ligand" representation, each peptide-like ligand residue is represented by a single circle. Only sidechains involved in hydrogen bonds or hydrophobic contacts with the protein are shown explicitly. The "schematic" representation for non-ligand residues means that each is represented by a single box with the residue name and number inside it. Note 2 ------ If accessibility option is selected, the shading behind each ligand atom will be according to that atom's solvent accessibility. Solvent accessibilities can be calculated by running the NACCESS program. This generates a .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. Note that, when running NACCESS you should use the -f and -h flags. Note 3 ------ 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. LINKED RESIDUES (see Note below) --------------- HIS-ASP <- Residue-pair 1 HOH-*** <- Residue-pair 2 <- Residue-pair 3 <- Residue-pair 4 <- Residue-pair 5 <- Residue-pair 6 <- Residue-pair 7 <- Residue-pair 8 <- Residue-pair 9 <- Residue-pair 10 Note ---- The above options allow residues that are not directly hydrogen-bonded to the ligand to be included in the plot, provided they are hydrogen-bonded to a residue that IS hydrogen-bonded to the ligand. The residues to be included by their residue type and the non-ligand residue to which they are H-bonded. For example, `HIS-ASP' will include any Asp residues that are H-bonded to a His which is H-bonded to the ligand. More generally, `HIS-***' will show any residue H-bonded to the HIS. Similarly, `HOH-***' will include any residues in the protein that are connected to the ligand via a water molecule. SIZES (All sizes are relative sizes given in Angstroms) ----- 0.33 <- Radius: Ligand atoms 0.33 <- Radius: Non-ligand atoms 0.40 <- Radius: Water molecules 1.15 <- Radius: Hydrophobic contact residues 0.80 <- Radius: Ligand residues in simple-residue representation 0.19 <- Line-thickness: Ligand bonds 0.13 <- Line-thickness: Non-ligand bonds 0.07 <- Line-thickness: Hydrogen bonds 0.07 <- Line-thickness: External covalent bonds TEXT SIZES (Relative sizes in Angstroms) ---------- 0.80 <- Residue names: Ligand residues 0.63 <- Residue names: Non-ligand residues 0.50 <- Residue names: Water molecule IDs 0.50 <- Residue names: Hydrophobic-interaction residues 0.50 <- Residue names: in simple-residue representation 0.31 <- Atom names: Ligand atoms 0.31 <- Atom names: Non-ligand atoms 0.44 <- Hydrogen-bond lengths COLOURS (Note: colour definitions are given at end of file) ------- CREAM <- Background colour of page PURPLE <- Ligand bonds [or ATOM - see Note] ORANGE <- Non-ligand bonds [or ATOM - see Note] OLIVE GREEN <- Hydrogen bonds PURPLE <- External covalent bonds BRICK RED <- Hydrophobic interactions ORANGE <- Accessibility shading: Buried atoms YELLOW <- Accessibility shading: Accessible atoms BLUE <- Nitrogen atoms RED <- Oxygen atoms BLACK <- Carbon atoms YELLOW <- Sulphur atoms TURQUOISE <- Water atoms PURPLE <- Phosphorus atoms PINK <- Iron atoms LIME GREEN <- All other atoms BLACK <- Atom edges BLACK <- Circles in simple-residue representation Note ---- If ATOM is entered as the colour of the bonds, the bonds will be coloured such that each half is of the colour of the atom bonded at that end. TEXT COLOURS (Note: colour definitions are given at end of file) ------------ BLACK <- Plot title BLACK <- Legends in key to symbols BLUE <- Residue names: Ligand residues BRICK RED <- Residue names: Non-ligand residues PURPLE <- Residue names: Water molecule IDs BLACK <- Residue names: Hydrophobic-interaction residues BLACK <- Atom names: Ligand atoms BLACK <- Atom names: Non-ligand atoms OLIVE GREEN <- Hydrogen bond lengths COLOUR DEFINITIONS ------------------ 0.0000 0.0000 0.0000 'BLACK '<- Colour 1 1.0000 1.0000 1.0000 'WHITE '<- Colour 2 1.0000 0.0000 0.0000 'RED '<- Colour 3 0.0000 1.0000 0.0000 'GREEN '<- Colour 4 0.0000 0.0000 1.0000 'BLUE '<- Colour 5 1.0000 1.0000 0.0000 'YELLOW '<- Colour 6 0.8000 0.5000 0.0000 'ORANGE '<- Colour 7 0.5000 1.0000 0.0000 'LIME GREEN '<- Colour 8 0.5000 0.0000 1.0000 'PURPLE '<- Colour 9 0.5000 1.0000 1.0000 'CYAN '<- Colour 10 1.0000 0.5000 1.0000 'PINK '<- Colour 11 0.3000 0.8000 1.0000 'SKY BLUE '<- Colour 12 1.0000 1.0000 0.7000 'CREAM '<- Colour 13 0.0000 1.0000 1.0000 'TURQUOISE '<- Colour 14 1.0000 0.0000 1.0000 'LILAC '<- Colour 15 0.8000 0.0000 0.0000 'BRICK RED '<- Colour 16 0.5000 0.0000 0.0000 'BROWN '<- Colour 17 0.9700 0.9700 0.9700 'LIGHT GREY '<- Colour 18 0.1000 0.5000 0.0000 'OLIVE GREEN '<- Colour 19 1.0000 1.0000 1.0000 'WHITE '<- Colour 20 MINIMIZATION PARAMETERS ----------------------- 10.00 <- Atom-atom clash parameter 0.20 <- Bond-atom clash parameter 200.0 <- Bond-overlap score 0.5 <- Weight for term giving H-bond deviation from ideal value 0.01 <- Weight for term giving non-bond dist deviation from ideal value 10.0 <- Weight for internal energies (atom clashes, etc) 15.0 <- Furthest move-distance for H-bonded groups (in Angstroms) 1.0 <- "Stretch factor" for H-bond lengths 1000 <- Number of loops for the minimization process 0.0 <- Terminate minimization if energy drops by less than this value N <- Random start for minimization routines - (Y/N)? 20.0 <- Weight for anchor-position energy term 5.0 <- Weight for interface-boundary energy term 2.0 <- Closest atom-distance to boundary representing interface 0.3 <- Weight for relative residue-positions energy term