# new feature: ISOSURFACE Kinemage file reader (for contact/clash dots)
#
#  -- colors are set from the kin file
#  -- parameters [cutoff, valueMin, valueMax, pointType]
#  -- valueMin -- minimum value to display
#  -- valueMax -- maxiumum value to display
#       color.equals("greentint") ? 4f        H-bond
#         : color.equals("blue") ? 0.35f       wide contact
#         : color.equals("sky") ? 0.25f        almost wide contact 
#         : color.equals("sea") ? 0.15f        close contact
#         : color.equals("green") ? 0.0f       contact
#         : color.equals("yellowtint") ? -0.1f small overlap
#         : color.equals("yellow") ? -0.2f     small overlap
#         : color.equals("orange") ? -0.3f     small overlap
#         : color.equals("red") ? -0.4f        almost bad overlap
#         : -0.5f);                            bad overlap
#  -- pointType:
#       0   all points
#   	1   'M' {McMc contacts}
#  	2   'S' {ScSc contacts}
#       3   'P' {McSc contacts}
#       4   'O' {Hets contacts}
#
#  -- dot size controllable via "set dotscale"
#  -- example:
#
#    isosurface 2bxaH-multi.kin  # all overlaps
#    isosurface parameters [0 -1 -0.1] 2bxaH-multi.kin # just non-H-bond overlaps
#    isosurface slab within 3.0 {2001:A}; display group contact(2001:A); zoom {displayed} 0
#   
# new feature: set VDW PROBE  --- sets VDW radii as follows
#   as per Word, et al, J. Mol. Biol. (1999) 285, 1711-1733
#       {_H}.vdw = 1.0;
#       {_H and connected(_C) and not connected(within(smiles,'[r6]'))}.vdw = 1.17;
#       {_C}.vdw = 1.75;
#       {_C and connected(3) and connected(_O)}.vdw = 1.65;
#       {_N}.vdw = 1.55;
#       {_O}.vdw = 1.4;
#       {_P}.vdw = 1.8;
#       {_S}.vdw = 1.8;
#
#   and returned to standard settings using   set vdw JMOL
#