Isosurface

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isosurface creates a new surface object from a map object.

Usage

 isosurface name, map, [,level [,(selection) [,buffer [,state [,carve [,source_state [,side [,mode ]]]]]]]]
  • name = the name for the new mesh isosurface object.
  • map = the name of the map object to use for computing the mesh.
  • level = the contour level. (default=1.0)
  • selection = an atom selection about which to display the mesh with an additional "buffer" (if provided). (default="")
  • state = the state into which the object should be loaded (default=1) (set state=-2 to append new surface as a new state)
  • carve = a radius about each atom in the selection for which to include density. If "carve= not provided, then the whole brick is displayed. (default=None)
  • source_state = the state of the map from which the object should be loaded. (default=0)
  • Front or back face. Triangle-winding/normal direction. (default=1)
  • mode = surface geometry (0: dots; 1: lines; 2: triangle triangle-normals; 3: triangle gradient-normals) (default=3)

Algorithm

PyMOL offers three different algorithms for isosurface generation. Each of these can be activated by the isosurface_algorithm setting

  • 0: Marching Cubes via VTKm (default) (requires VTKm)
  • 1: Marching Cubes basic (fallback if VTKm not installed)
  • 2: Marching tetrahedra (legacy)

Examples

fetch 1oky, type=2fofc, async=0
isosurface 1okySurf, 1oky_2fofc

With carving at 2 Angstrom around the molecular model:

fetch 1oky, async=0
fetch 1oky, type=2fofc, async=0
isosurface 1okySurf, 1oky_2fofc, 1.0, (1oky), carve=2.0

Notes

If there exists a non-map object with the same name, then the new surface will overwrite that object. Surface objects can be appended onto existing surface objects using the aforementioned state argument.

See Also