Surfaces

  • cavity_cull (integer, default: 10) is the threshold below which isolated clusters of points will be excluded from the surface representation. These are generally interior pockets inside of proteins.
  • solvent_radius (float, default: 1.4) is the radius used in computing the surface as well as a number of other solvent-dependent properties within PyMOL.
  • surface_best (float, default: 0.25) is a tuning parameter that should not need to be modified.
  • surface_carve_cutoff (float, default: 0.0) controls the cutoff distance from surface_carve_selection atoms which surface points must meet to be included in the carved surface.
  • surface_carve_normal_cutoff (float, default: -1.0) controls the dot product threshold from surface_carve_selection atoms which surface points must meet to be included in the carved surface.
  • surface_carve_selection (string, default: blank) is the named selection of atoms about which the surface is carved.
  • surface_carve_state (integer, default: 0) is the controlling state for surface carving. By default, the corresponding coordinate set state is used.
  • surface_circumscribe (integer 0-120, default: -1) is a parameter that can be used to force approximate surfaces to track concave regions more closely, but this can degrade visual aesthetics. By default, this setting is automatically activated to improve the quality of certain surface types.
  • surface_clear_cutoff (float, default: 0.0) controls the cutoff distance from surface_clear_selection atoms which surface points must meet to be excluded for the carved surface.
  • surface_clear_selection (string, default: blank) is the named selection of atoms about which the carved surface avoids.
  • surface_clear_state (integer, default: 0) is the controlling state for clearing.
  • surface_color (color, default: -1) controls the surface color. By default, surfaces assume the color of the underlying atom.
  • surface_debug (integer, default: 0) activates debugging mode for development.
  • surface_miserable (float, default: 2.0) is a tuning parameter that should not need to be modified.
  • surface_mode (integer, default: 0) controls what atoms are considered when generating the surface:
    • 0 = consider atoms based on their ignore and exfoliate flags.
    • 1 = consider all atoms
    • 2 = condider only non-hydrogen atoms
  • surface_normal (float, default: 0.5) is a tuning parameter that should not need to be modified.
  • surface_optimize_subsets (boolean, default: on) tells PyMOL that it can compute a subsurface without rendering the entire surface. This option should be disabled when trying to effectively multiple surface from identical objects.
  • surface_poor (float, default: 0.85) is a tuning parameter that should not need to be modified.
  • surface_proximity (boolean, default: on) controls whether or not PyMOL draws triangle with one or two vertices belonging to atoms not currently shown.
  • surface_quality (integer: -4 to 4, default: 0) controls how many triangles are used to render the surface. Surface qualities of 2 and above are only practical for very small systems. Surface qualities below 2 are only practical for large globular systems.
  • surface_ramp_above_mode (boolean, default: off) controls whether surfaces are colored by the value at the surface or one solvent radius above the surface.
  • surface_solvent (boolean, default: off) controls whether or not solvent accessible surfaces are generated.
  • surface_trim_cutoff (float, default:0.2) is a tuning parameter that should not need to be modified.
  • surface_trim_factor (float, default:2.0) is a tuning parameter that should not need to be modified.
  • surface_type (integer, default: 0) controls what kind of surface is generated:
    • 0 = a solid surface via PyMOL’s conventional algorithm.
    • 1 = a dot surface via PyMOL’s conventional algorithm.
    • 2 = a triangle mesh surface via PyMOL’s conventional algorithm.
    • 3 = a solid surface using a deterministic algorithm better suited to dynamic surface animations.
    • 4 = a solid surface using the algorithm from 3 with different weightings.
    • 5 = a solid surface where all points are generated from pairwise scribed intersections instead of virtual solvent atoms.
  • triangle_max_passes (integer, default: 5) controls how much time PyMOL is allowed to spend attempting to resolve problematic surface regions.
 
setting/surface.txt
 
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