SURFNET parameters

3. OUTPUT FILES

Each line below the OUTPUT FILES line, up until the first blank line, defines each different output to be created by SURFNET.

            <----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      1    2389   100.0       1        10        0.1
inhibitor    S   2390    2480   100.0       2        10        0.1
waters       S   2481    2713   100.0       3        10        0.1
inhibitor_a  A   2390    2480     0.0      10        10        0.3
inhibitor_b  B   2390    2480     0.0      10        10        0.2  SOLID
gaps         G      2       1   100.0       4        10        0.1  SOLID

A separate output file is created for each line defined. The file's name will be the name defined in the Filename column (ie the first column), but with a .srf extension. (For example, the first file would be called protein.srf).

If you opt to have the output also generated in one of the molecular graphics package formats (eg QUANTA, SYBYL, O, etc.), an additional file with the appropriate extension will also be generated, as follows:-

.cnt - SYBYL contour-file format


.den - CCP4 density map (which can be coverted to FRODO and O formats using the CCP4 program MAPPAGE or Gerard Kleywegt's MAPMAN program)


.grd - InsightII grid-file format


.mbk - QUANTA brick-map format

Up to fifty output files can be defined, each on a separate line, starting on the line after OUTPUT FILES. A blank line terminates the list.

The information on each line is entered in free-format columns. The column headings above this section provide a guide the information to be entered.

i. Parameters applying to SURFNET only

• Filename - The filename (already mentioned) identifies each surface or object to be plotted, so no two names should be the same or this will result in an error.

• File type - The file type specifies the type of surface or object this is. The type is defined by one of the following letters:-

  A - Atoms. For plotting atoms by SURFPLOT as either points or spheres.

  a - As A above, but with colours of atoms defined by the value in the B-factor column of the PDB file.

  B - Bonds between atoms. Each bond will be plotted by SURFPLOT as a line of a given thickness. Bonds between atoms in the PDB file are computed using a simple distance cut-off.

  C - Contours generated on the basis of atom density.

  E - Energy. Contours generated on the basis of atomic B-values.

  G - Gaps between one molecule and another, or between all atoms of the same molecule. There should only be one file of this type defined, and it should be put last.

  J - Join between each atom and the one directly after it in the PDB file.

  P - Pair distribution where each sidechain in the PDB file, shown by bonds, is shown separately from any other sidechain - ie not connected irrespective of how close they are. This option is only for use in the special case where all the sidechains are of the same residue type).

  S - Surface contours generated so that the van der Waals surface of the molecule is given by a contour level of 100.0.

  % - As C above, but with all density values adjusted such that each represents the \%-tage of values lower than it.

  Only file types C, E, G, S and % result in maps for QUANTA, SYBYL, O, etc..

  For surface files of type S, if there is an asterisk * between the filename in column 1 and the S option in column 2, the atomic radii for used each atom in the input PDB file will be the values given in that atom's B-factor column.

• Atom range - The atom range entered in columns 3 and 4 defines which atoms in the PDB file are associated with each surface to be generated. In the example above, the protein surface is defined by atom numbers 1-2389, the inhibitor by atom numbers 2390-2480, and so on.

  Where you need to define two or more atom ranges for the same, you would do it as follows. Say that the parts of the protein you are interested in involve atoms 1-789, 982-1614 and 1690-2402. That is, the atom-ranges are not contiguous. In this case, you would define the protein surface as:-

  ---

  OUTPUT FILES
  protein      S      1     789   100.0       1        10        0.1
     "         S    982    1614   100.0       1        10        0.1
     "         S   1690    2402   100.0       1        10        0.1
  

  ---

  The ditto marks indicate that the following ranges belong to the same surface. You cannot have dittos as either the first file name, nor can they apply to a Gap map. There is a limit on the number of ditto ranges that can apply to a single file.

  For a Gap map (type G) the range has a special meaning. It refers not to an atom range but to the files in the lines above; the two numbers define between which surfaces the gaps are to be generated. So, if the range is entered as

  gaps      G    1   3
  

  the program will generate gap contours between the atoms of the first and third files listed under the OUTPUT FILES heading.

  There are two special cases:-

  • Firstly, if the second of the two numbers is zero:-

    gaps      G    1   0
    

    the gaps will be generated between the atoms of first file and the atoms of all the other files.

  • In the second special case, if both numbers are zero:-

    gaps      G    0   0
    

    then the gaps will be generated between all pairs of atoms. This second case is used to get the clefts and cavities in a given protein molecule.

ii. Parameters applying to SURFACE only

• Contour level - The contour level is relevant only to surface maps (ie file types C, E, G, S and %).

  For van der Waals surfaces (type S) and gap regions (G) you should use a contour level of 100.0.

  A negative contour level will not produce a .grf file and hence the object will not be plotted by SURFPLOT. This may be useful if the object involved is very large and exceeds the SURFACE programs' array capacity.

  For contour files (file type C), which give contours based on the density of atoms/data points in the PDB file, it may be difficult to tell in advance what the contour levels should be. In this case a percent-sign % can be used to define the contour level as a given percentage of the maximum density value. For example, the entry might be as follows:-

  OUTPUT FILES
  data1        C      1   10000    20.0%      1        10        0.1
  data2        C      1   10000    50.0%      5        10        0.1
  

  This would produce two 3D contour files of the same data, the first contoured at 20% of the maximum density value, and the other at 50% of the maximum density value.

iii. Parameters applying to SURFPLOT only

• Foreground and background colour or shade - The plots produced by SURFPLOT can show the 3D object in question and/or three orthographic projections onto three back walls. The foreground and background colours can be independently defined for each object in the PostScript and Raster3D output.

  The colours are:

  0 = White
  1 = Yellow
  2 = Cyan
  3 = Lime green
  4 = Green
  5 = Blue
  6 = Pink
  7 = Orange
  8 = Red
  9 = Purple
  10 = Black
  

  For black-and-white output, the numbers correspond to a grey scale going from 0 for white to 10 for black.

  In addition to these colours, there are also some ``special'' values that can be entered for certain specific effects on the objects being plotted. These are:-

  • No plot - To cause an object's foreground or background image not to be plotted at all, enter -999 for the corresponding colour. Thus if -999 is entered as the foreground colour, the foreground object will not be plotted. Similarly, if the background colour is -999 the back projections of the object will not be drawn.

  • A `sketch' representation of surfaces - For a surface defined as SOLID in Column 9, and plotted in black-and-white, a negative colour will result in all surface polygons being white, giving a sketched, cartoon appearance.

  • Atoms as points - Atoms (in type A files) can be plotted as points, rather than as spheres, by entering a negative value for the colour (ie -10 to -1).

  • Atoms in single colour - The default atom colours are determined by the atom types (ie black for carbon, red for oxygen, blue for nitrogen, etc.). If, however, you want all the atoms to be of one colour, as defined here in columns 6 and 7, then set the line-width (see Column 8 below) to a negative value.

  • Bonds in single colour - The default bond colours are determined by the atoms at either end (see Atoms in single colour above). If, however, you want all the bonds to be of one colour, as defined here in columns 6 and 7, then set the colours to a negative value. For example, a colour of -4 in column 6 will plot all the foreground bonds as green. Any positive number will show the bonds according to the atom types at either end.

  • Shadow projections - If a G is entered after the background colour, then the background object will be displayed in grey (ie as shadow).

• Line width - For surfaces and bonds, the line width defines the thickness of the lines used to draw the given object (in Ångströms). Thick lines (say, 0.3Å) are appropriate for showing bonds. The thickness of the lines projected back onto the three back walls is a fifth of the thickness of the foreground lines. The lines used for drawing wire-cage contours are one tenth of the value entered here.

  For atom objects (types A and a) the line width defines the atom radii.

  Furthermore, there are two special cases:-

  • Dashed lines - Dashed lines will be produced for bond lines (file types B, J and P) if the line width is entered as a negative number.

  • Atoms in single colour - By entering a negative line-width, atom colours can be set from the default values to the colours defined in columns 6 and 7 (see above).

• SOLID/WIRE - The final option determines whether a contour object (type C, E, G, or S) is to be plotted as a wire-frame picture, or as a solid shaded object. If the column is left blank the default option is WIRE.

  For other file types, the SOLID/WIRE option has special meanings:-

  • Spheres in back-projections - Atoms (file types A and a) are generally plotted as spheres in the foreground and as circles in the back projections. The SOLID option shows the atoms on the back projections also as spheres.

  • Ball-and-stick bonds - To give a ball-and-stick effect, the bonds between atoms need to be drawn joining the atom surfaces rather than the atom centres. The SOLID option on type B files achieves this by truncating all the bonds at each end to the surface of the attached atom. This allows the type A and B files to be used together to generate a ball-and-stick representation of a molecule.

SURFNET parameters