Parameters for SURFNET (surfnet.par) ---------------------- TITLE IL8 INPUT FILE il8.pdb Output files listed below. The information entered for each is as follows. The numbers in square brackets refer to the notes at the end of the file. The program names indicate which programs need to be rerun when any of the parameters are changed. <----SURFNET----><-SURFACE-><----------SURFPLOT------------> Foregrnd Backgrnd Atom range colour colour Line File 1st Last Contour /shade /shade width SOLID Filename type[1] atom atom level[2] (0-10)[3] (0-10)[3] [4] /WIRE OUTPUT FILES protein S 7 2402 100.0 11 10 0.1 gaps G 0 0 100.0 8 10 0.1 WIRE Program parameters ------------------ SURFNET 0.0 0.0 0.0 <- Origin of grid box (to use: set atom range below to 0 0) -1000 10000 <- Atom range defining grid bounds (0 0 to use origin above) 6.0 6.0 6.0 <- Additional boundary round atom-range/origin (Angstroms) 0.80 <- Grid separation 1.4 <- Minimum radius for gap spheres (in Angstroms) 4.0 <- Maximum radius for gap spheres (in Angstroms) C <- (C)CP4, (I)nsightII, (Q)uanta, (S)ybyl contour files, or (N)one Y <- Calculate gap volume - (Y/N)? 1.0 <- Scaling factor SURFACE (Currently no additional parameters) SURFPLOT C <- (C)olour/(B)&W Postscript file, (P)DB-format, (R)aster3D 11 <- Background colour 12 <- Colour of "walls" in back-projections A <- (F)loor, (L)eft wall, (R)ight wall, (A)ll three, (N)one Y <- Display foreground object (Y/N)? Y <- Margin round object - (Y/N)? 0.20 <- Atom radius (in Angstroms) for plot - NOT USED N <- Print sequential numbers by the atoms (Y/N)? Y <- Maintain x-,y-,z-axes (ignore matrix below) (Y/N)? 0.0 <- Rotation about x-axis 0.0 <- Rotation about y-axis 0.0 <- Rotation about z-axis 1.0000 0.0000 0.0000 <- 0.0000 1.0000 0.0000 <- Transformation matrix 0.0000 0.0000 1.0000 <- 50.0 100.0 100.0 <- Position of light-source 40 32 <- Raster3D size, number of tiles in x and y (Max: 80 64) N <- Infinite planes for back wall(s) in Raster3d (Y/N)? --------------------------------------------------------------------------- Notes:- Note 1. type is one of the following characters:- A - Atoms only, each atom will be plotted as a sphere a - As for A, but atoms coloured according to B-factor (0-80) B - Bonds between atoms C - Contours generated according to the density of atoms E - Contours generated according to the B-values G - Gap map (see below) J - Each atom coordinate is joined to the one before and after it P - Pairs distribution where each sidechain is shown (by bonds joining the atoms) separately S - Surface contours at van der Waals radius of each atom (contour level of 100.0). If an asterisk, *, follows the S, then the radius of each atom will be picked up from the B-value column of the PBD file. Otherwise, the default van der Waals radii are used. % - As C above, but all density values in the output grid are adjusted such that the value at each grid-point gives the percentage of non-zero grid-points with lower values. For a Gap map (type G) the first number after it refers to which file is to be used for generating gaps from. If this is a zero, then gaps are required between ALL atoms. The second number after the G should be a zero. For a surface contour (type S), each atom/data-point can have its own radius defined in the B-value column of the PDB file. This will be used if there is an asterisk, *, before the S. Note 2. The contour level can be entered as a percentage by entry of a % after the contour value. Note 3. Colours can be entered separately for the foreground and projected objects. The colours are as follows: 0=white, 1=yellow, 2=cyan, 3=lime green, 4=green, 5=blue, 6=pink, 7=orange, 8=red, 9=purple, 10=black, 11=Light blue, 12=Cream If the colour PostScript option in SURFPLOT below is set to N, the colour values will be interpreted as grey shades (0=white to 10=black). If the colour is entered as -999 for the foreground object, the object will not be displayed. Similarly, for the background projections For "atom" objects (displayed as spheres), if the colour is set between -1 and -10, a single point, of the corresponding colour, will be plotted rather than a sphere. For SOLID surfaces, if in black and white, a negative colour causes all polygons to be shaded white, giving a sketched, cartoon appearance. If a 'G' is entered after the background colour, then the background object will be displayed in grey (ie as shadow) for a colour PostScript file. Note 4. Line widths can be set to any real number (a sensible range being 0.0-5.0). The widths of the projected lines will be a fifth of those for the foreground object.